Schema for Affy U95 - Alignments of Affymetrix Consensus/Exemplars from HG-U95
  Database: hg19    Primary Table: affyU95    Row Count: 13,864   Data last updated: 2010-11-29
Format description: Summary info about a patSpace alignment
fieldexampleSQL type info description
bin 591smallint(5) unsigned range Indexing field to speed chromosome range queries.
matches 2085int(10) unsigned range Number of bases that match that aren't repeats
misMatches 7int(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 92int(10) unsigned range Number of 'N' bases
qNumInsert 10int(10) unsigned range Number of inserts in query
qBaseInsert 596int(10) unsigned range Number of bases inserted in query
tNumInsert 20int(10) unsigned range Number of inserts in target
tBaseInsert 12865int(10) unsigned range Number of bases inserted in target
strand -char(2) values + or - for strand. First character query, second target (optional)
qName 41861_atvarchar(255) values Query sequence name
qSize 2841int(10) unsigned range Query sequence size
qStart 4int(10) unsigned range Alignment start position in query
qEnd 2784int(10) unsigned range Alignment end position in query
tName chr1varchar(255) values Target sequence name
tSize 249250621int(10) unsigned range Target sequence size
tStart 879582int(10) unsigned range Alignment start position in target
tEnd 894631int(10) unsigned range Alignment end position in target
blockCount 21int(10) unsigned range Number of blocks in alignment
blockSizes 598,90,139,65,40,53,37,140,...longblob   Size of each block
qStarts 57,670,760,1009,1118,1405,1...longblob   Start of each block in query.
tStarts 879582,880436,880897,881780...longblob   Start of each block in target.

Connected Tables and Joining Fields
        hg19.knownToU95.value (via affyU95.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
59120857092105962012865-41861_at284142784chr124925062187958289463121598,90,139,65,40,53,37,140,184,104,45,42,83,37,90,22,88,47,90,153,37,57,670,760,1009,1118,1405,1458,1495,1635,1834,1938,2007,2049,2173,2250,2340,2384,2472,2557,2647,2800,879582,880436,880897,881780,881889,886527,886581,887379,887791,888564,889161,889230,889383,891347,891505,892273,892317,892478,89 ...
5926480053224410+38432_at9860703chr1249250621948809949920710,23,42,69,394,156,7,0,10,33,75,144,539,696,948809,948820,948844,948887,949363,949757,949913,
592625300001407+1107_s_at6340628chr1249250621948878949913278,550,0,78,948878,949363,
592609890590295634729218+33454_at728407260chr124925062195558199149662172,101,87,20,56,160,29,180,225,207,72,132,195,142,41,149,106,49,45,79,18,92,106,185,154,138,128,115,120,37,300,193,54,162,230,1 ...0,172,292,462,482,539,699,744,924,1149,1356,1443,1575,1770,1930,1971,2120,2226,2405,2573,2652,2685,2777,2883,3069,3223,3361,3489 ...955581,957580,957700,970684,976044,976100,976552,976597,976857,977335,978618,978705,978917,979202,979362,979488,979713,980540,98 ...
59394410872261740-34916_s_at105921036chr1249250621114672411494968288,4,117,197,67,102,123,134,23,312,317,434,631,698,800,923,1146724,1147091,1147095,1147321,1148017,1148371,1149042,1149362,
59387810230061739-34917_at13580902chr1249250621114687111495127134,129,197,67,102,123,150,456,590,719,916,983,1085,1208,1146871,1147083,1147321,1148017,1148371,1149042,1149362,
594207100649205155870+34462_at234902340chr1249250621121940412274092066,353,208,123,14,10,44,89,164,99,77,41,79,58,29,213,238,17,37,176,0,66,419,627,751,766,777,821,910,1074,1173,1251,1292,1371,1429,1579,1807,2069,2111,2164,1219404,1221305,1222147,1222488,1222611,1222625,1222635,1222887,1223052,1223318,1225650,1225727,1225856,1226016,1226274,1226648, ...
594202544003661710979-163_at2177422177chr124925062112715001284548194,194,187,207,168,132,78,68,77,140,70,94,139,104,122,70,176,19,20,0,4,207,394,601,769,901,979,1047,1124,1264,1334,1428,1567,1671,1793,1863,2095,2115,1271500,1271505,1271708,1273356,1273648,1273901,1274741,1274961,1275115,1275417,1275626,1275789,1277046,1277432,1277742,1278068, ...
59411335020046212753-35219_at1444131413chr12492506211288070129016115191,87,294,81,224,12,81,77,40,137,21,30,7,15,41,31,264,369,663,745,970,982,1063,1140,1180,1317,1338,1368,1375,1390,1288070,1288303,1288397,1288692,1288773,1288997,1289227,1289409,1289572,1289733,1289871,1290065,1290096,1290104,1290120,
741025005151521164603+38950_r_at126201228chr12492506211567559163323812194,131,140,89,44,41,28,55,78,108,72,96,0,194,325,465,589,633,700,743,798,928,1036,1132,1567559,1631380,1631578,1631785,1631909,1632345,1632412,1632455,1632586,1632818,1633046,1633142,

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

Affy U95 (affyU95) Track Description
 

Description

This track shows the location of the consensus and exemplar sequences used for the selection of probes on the Affymetrix HG-U95Av2 chip. For this chip, probes are predominantly designed from consensus sequences.

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=0.3 -minAli=0.95 -nearTop=0.005

Credits

Thanks to Affymetrix for the data underlying this track.