Schema for Affy U133 - Alignments of Affymetrix Consensus/Exemplars from HG-U133
  Database: hg38    Primary Table: affyU133    Row Count: 50,481   Data last updated: 2015-01-08
Format description: Summary info about a patSpace alignment
fieldexampleSQL type info description
bin 585smallint(5) unsigned range Indexing field to speed chromosome range queries.
matches 509int(10) unsigned range Number of bases that match that aren't repeats
misMatches 4int(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 23int(10) unsigned range Number of 'N' bases
qNumInsert 3int(10) unsigned range Number of inserts in query
qBaseInsert 41int(10) unsigned range Number of bases inserted in query
tNumInsert 2int(10) unsigned range Number of inserts in target
tBaseInsert 141int(10) unsigned range Number of bases inserted in target
strand -char(2) values + or - for strand. First character query, second target (optional)
qName U133B:225995_x_at;varchar(255) values Query sequence name
qSize 637int(10) unsigned range Query sequence size
qStart 26int(10) unsigned range Alignment start position in query
qEnd 603int(10) unsigned range Alignment end position in query
tName chr1varchar(255) values Target sequence name
tSize 248956422int(10) unsigned range Target sequence size
tStart 14361int(10) unsigned range Alignment start position in target
tEnd 15038int(10) unsigned range Alignment end position in target
blockCount 4int(10) unsigned range Number of blocks in alignment
blockSizes 93,144,229,70,longblob   Size of each block
qStarts 34,132,278,541,longblob   Start of each block in query.
tStarts 14361,14454,14599,14968,longblob   Start of each block in target.

Connected Tables and Joining Fields
        hg38.knownToU133.value (via affyU133.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
58550940233412141-U133B:225995_x_at;63726603chr12489564221436115038493,144,229,70,34,132,278,541,14361,14454,14599,14968,
5853355170122854911608-U133B:225035_x_at;363503548chr124895642214381294831773,375,71,165,303,360,198,661,201,1,260,250,74,73,112,154,163,87,165,540,647,818,1123,1484,1682,2343,2545,2546,2808,3058,3133,3206,3318,3472,14381,14454,14969,15075,15240,15543,15903,16104,16853,17054,17232,17492,17914,17988,18267,24737,29320,
5854156140831618293-U133B:226340_x_at;431834274chr1248956422143991874518690,10,32,33,376,4,5,15,5,11,7,41,277,859,141,51,443,1253,44,735,746,779,813,1190,1195,1201,1217,1223,1235,1243,1285,1564,2423,2565,2617,3062,14399,15089,15099,15131,15164,15540,15544,15549,15564,15569,15580,15587,15628,15906,16857,16998,17049,17492,
58551801401671038129-U133B:231811_at;539905399chr1248956422196882507811131,26,1300,6,4,11,4,7,358,3359,155,0,132,159,1460,1467,1472,1484,1489,1497,1856,5244,19688,19819,19845,21145,21151,21155,21166,21170,21177,21535,24923,
58546850140000-U133B:236841_at;4870487chr124895642227542280291487,0,27542,
5857233061112+U133B:228609_at;7330733chr124895642228444291783145,125,462,0,145,271,28444,28591,28716,
73258521056221176810-U133B:231949_at;2676122676chr1248956422875432670154511,1583,303,265,0,512,2095,2399,87543,88054,266447,266750,
58674020260000-U133B:225899_x_at;85170838chr12489564221347721355401768,13,134772,
58653460272363898-U133B:225995_x_at;6370603chr12489564221848771863424242,229,70,26,34,278,541,611,184877,185120,185489,186316,
5863355200126647911601-U133B:225035_x_at;363503548chr124895642218489719999915453,71,165,303,559,661,201,1,512,47,26,73,112,154,163,87,540,647,818,1123,1682,2343,2545,2546,3058,3106,3133,3206,3318,3472,184897,185490,185596,185761,186064,186626,187375,187576,187754,188438,188485,188511,188790,195262,199836,

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

Affy U133 (affyU133) Track Description
 

Description

This track shows the location of the consensus and exemplar sequences used for the selection of probes on the Affymetrix HG-U133A and HG-U133B chips.

Methods

Consensus and exemplar sequences were downloaded from the Affymetrix Product Support and mapped to the genome using blat followed by pslReps with the parameters:

   -minCover=0.5 -minAli=0.97 -nearTop=0.005

Credits

Thanks to Affymetrix for the data underlying this track.