Schema for Affy RAE230 - Alignments of Affymetrix Consensus Sequences from RAE230
  Database: rn4    Primary Table: affyRAE230    Row Count: 29,991   Data last updated: 2006-04-12
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 1390smallint(5) unsigned range Indexing field to speed chromosome range queries.
matches 867int(10) unsigned range Number of bases that match that aren't repeats
misMatches 0int(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 3int(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 2int(10) unsigned range Number of inserts in target
tBaseInsert 10585int(10) unsigned range Number of bases inserted in target
strand -char(2) values + or - for strand. First character query, second target (optional)
qName A:1367452_atvarchar(255) values Query sequence name
qSize 1013int(10) unsigned range Query sequence size
qStart 127int(10) unsigned range Alignment start position in query
qEnd 997int(10) unsigned range Alignment end position in query
tName chr10varchar(255) values Target sequence name
tSize 110718848int(10) unsigned range Target sequence size
tStart 105608096int(10) unsigned range Alignment start position in target
tEnd 105619551int(10) unsigned range Alignment end position in target
blockCount 3int(10) unsigned range Number of blocks in alignment
blockSizes 664,72,134,longblob   Size of each block
qStarts 16,680,752,longblob   Start of each block in query.
tStarts 105608096,105615316,105619417,longblob   Start of each block in target.

Connected Tables and Joining Fields
        rn4.rgdGene2ToRAE230.value (via affyRAE230.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
139086700300210585-A:1367452_at1013127997chr101107188481056080961056195513664,72,134,16,680,752,105608096,105615316,105619417,
70197520031100+A:1367452_at101381007chr51730962091532545015326448280,918,8,89,15325450,15325530,
7381605101111811011-A:1367453_at162351623chr8129041809201641432017677110539,72,183,123,116,109,61,27,190,197,0,539,611,794,917,1033,1142,1204,1231,1421,20164143,20166283,20166481,20167858,20168061,20168269,20168804,20168865,20168893,20176574,
103831930185151716217-A:1367455_at324383229chr517309620959472099594915321860,606,155,156,309,213,123,165,113,136,134,103,132,131,143,173,112,252,14,79,685,840,996,1305,1518,1641,1806,1919,2055,2189,2292,2424,2555,2698,2871,2983,59472099,59472162,59472917,59474367,59474684,59475188,59475985,59476210,59476855,59477713,59477929,59480346,59482272,59484462,59 ...
23622121002823626278+A:1367456_at215202152chr22582075402329432132329716409202,95,64,32,78,106,94,1256,222,0,203,298,362,394,472,578,672,1930,232943213,232943415,232958660,232958820,232963883,232965140,232967980,232970162,232971418,
1274182123526171013021-A:1367457_at190801891chr10110718848903179569033286112208,498,143,61,150,147,195,137,91,59,68,127,17,232,730,873,934,1084,1231,1426,1563,1654,1713,1781,90317956,90318164,90319406,90320071,90321187,90323772,90324732,90325034,90325276,90326008,90329789,90332734,
1765155530511103061-A:1367458_at158101564chr517309620915475040515475502912612,219,174,102,74,71,48,66,32,106,14,45,17,630,849,1023,1125,1199,1270,1318,1384,1416,1522,1536,154750405,154751017,154751312,154751594,154751799,154751997,154752151,154752639,154752793,154753044,154754969,154754984,
9321751003233414586-A:1367459_at180001786chr1011071884845515761455321308701,179,175,231,125,111,184,77,14,716,896,1072,1303,1428,1539,1723,45515761,45516462,45516641,45516816,45517172,45517483,45517674,45532053,
1472108004221024507-A:1367460_at212722116chr1797296363778434807787009913514,379,55,145,172,100,85,47,199,135,100,108,73,11,526,905,960,1105,1277,1377,1463,1510,1709,1844,1944,2052,77843480,77843994,77844464,77844657,77847476,77849579,77852803,77852888,77853455,77854778,77857928,77860171,77870026,
23732281401002130757-A:1367461_at327003270chr126791088617219966917223369622380,156,90,146,120,145,180,228,121,161,97,146,147,108,120,138,93,115,170,230,150,29,0,380,536,626,772,892,1037,1217,1445,1566,1727,1824,1970,2117,2225,2345,2483,2576,2691,2861,3091,3241,172199669,172200798,172201516,172202237,172204327,172205680,172207316,172207665,172210690,172211865,172213495,172215270,17221577 ...

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

Affy RAE230 (affyRAE230) Track Description
 

Description

This track shows the location of the consensus sequences used for the selection of probes on the Affymetrix RAE230A and RAE230B chips.

Methods

Consensus sequences were downloaded from the Affymetrix Product Support and mapped to the genome with blat followed by pslReps using the parameters -minCover=0.3, -minAli=0.95 and -nearTop=0.005.

Credits

Thanks to Affymetrix for the data underlying this track.