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Platform GPL17677 Query DataSets for GPL17677
Status Public on Sep 05, 2013
Title Illumina MaizeSNP50 BeadChip
Technology type oligonucleotide beads
Distribution custom-commercial
Organism Zea mays
Manufacturer Illumina, Inc.
Manufacture protocol See manufacturer's website.
 
 
Web link http://support.illumina.com/array/array_kits/maizesnp50_dna_analysis_kit.ilmn
Citation(s) 22174790
Submission date Sep 03, 2013
Last update date Sep 05, 2013
Contact name Eva Bauer
E-mail(s) e.bauer@tum.de
Phone ++49 8161 715243
Organization name Technical University of Munich
Department Plant Breeding
Street address Liesel-Beckmann-Str. 2
City Freising
ZIP/Postal code 85354
Country Germany
 
Samples (2290) GSM1221233, GSM1221234, GSM1221235, GSM1221236, GSM1221237, GSM1221238 
Series (1)
GSE50558 Intraspecific variation of recombination rate in maize

Data table header descriptions
ID SNP name as originally provided by Illumina with array information
IlmnID SNP Illumina ID as originally provided by Illumina with array information
RSID SNP RSID
SSID SNP SSID
B73_v2_chr Chromosome assignment in B73 reference sequence v2 according to MaizeGDB
B73_v2_BP Position in bp in B73 reference sequence v2 according to MaizeGDB
IlmnStrand Illumina strand as originally provided by Illumina with array information
SNP SNP alleles as originally provided by Illumina with array information
AddressA_ID AddressA_ID as originally provided by Illumina with array information
AlleleA_ProbeSeq AlleleA_ProbeSeq as originally provided by Illumina with array information
AddressB_ID AddressB_ID as originally provided by Illumina with array information
AlleleB_ProbeSeq AlleleB_ProbeSeq as originally provided by Illumina with array information
GenomeBuild GenomeBuild as originally provided by Illumina with array information
B73_v1_chr Chromosome assignment as originally provided by Illumina with array information
B73_v1_MapInfo Position assignment as originally provided by Illumina with array information
Ploidy Ploidy
Species Species
Source Sequence source as originally provided by Illumina with array information
SourceVersion Sequence source version as originally provided by Illumina with array information
SourceStrand Sequence source strand as originally provided by Illumina with array information
SourceSeq Source sequence as originally provided by Illumina with array information
TopGenomicSeq Top genomic sequence as originally provided by Illumina with array information
BeadSetID Bead set ID as originally provided by Illumina with array information
Exp_Clusters Expected number of clusters as originally provided by Illumina with array information
MaizeSNP50_A.bpm.GenTrain Score GenTrain score - Measure of the cluster quality for the SNP
MaizeSNP50_A.bpm.Cluster Sep Cluster separation - Measure of the cluster separation for the SNP that ranges between 0 and 1
SPOT_ID SNP RSID

Data table
ID IlmnID RSID SSID B73_v2_chr B73_v2_BP IlmnStrand SNP AddressA_ID AlleleA_ProbeSeq AddressB_ID AlleleB_ProbeSeq GenomeBuild B73_v1_chr B73_v1_MapInfo Ploidy Species Source SourceVersion SourceStrand SourceSeq TopGenomicSeq BeadSetID Exp_Clusters MaizeSNP50_A.bpm.GenTrain Score MaizeSNP50_A.bpm.Cluster Sep SPOT_ID
abph1.15 abph1.15-0_T_F_1605158166 rs131175417 ss196415051 2 27482871 TOP [A/G] 56660487 TTCACCCTAGCTTGGTAGCAGCTAGCTAGCAGTATGATGCTGCTGATGCC 1 0 0 diploid Zea mays Panzea 0 TOP NNNNNTTCCTTTCACCCTAGCTTGGTAGCAGCTAGCTAGCAGTATGATGCTGCTGATGCC[A/G]ACAGAATGAGATTCGTGCATGCAGGAGTCGTCCAGGCTGAAGGAGATCCCCGTGGTGATC NNNNNTTCCTTTCACCCTAGCTTGGTAGCAGCTAGCTAGCAGTATGATGCTGCTGATGCC[A/G]ACAGAATGAGATTCGTGCATGCAGGAGTCGTCCAGGCTGAAGGAGATCCCCGTGGTGATC 233 3 0.8677401 0.6169883 rs131175417
abph1.22 abph1.22-0_T_F_1605156962 rs131175416 ss196415049 2 27482777 TOP [A/C] 15772361 AGATCCCCGTGGTGATCATGTCCTCAGAGAACGTGCCGACAAGGATCAAC 1 2 27403892 diploid Zea mays Panzea 0 TOP AGGCTGAAGGAGATCCCCGTGGTGATCATGTCCTCAGAGAACGTGCCGACAAGGATCAAC[A/C]GGTTAGTTCGTACTTCGTAAACGCATATACCTMTTCGTTCATCSTTATACTGCATATTTT AGGCTGAAGGAGATCCCCGTGGTGATCATGTCCTCAGAGAACGTGCCGACAAGGATCAAC[A/C]GGTTAGTTCGTACTTCGTAAACGCATATACCTMTTCGTTCATCSTTATACTGCATATTTT 233 3 0.8216856 0.4371691 rs131175416
ae1.4 ae1.4-0_B_R_1605157313 rs131175700 ss196416189 5 168468333 BOT [T/C] 68607395 CCTCCAGTTCATCCGACTGGAATTGAGCCGAGTCAGCCCTTGATGCGAGG 1 5 167889682 diploid Zea mays Panzea 0 TOP CCATGCGMGCGGCGGCYGCGGCCRGGAAGGCGGYCATGGTTCCTGAGGGCGAGAATGATG[A/G]CCTCGCATCAAGGGCTGACTCGGCTCAATTCCAGTCGGATGAACTGGAGGTTCGTCATCC CCATGCGMGCGGCGGCYGCGGCCRGGAAGGCGGYCATGGTTCCTGAGGGCGAGAATGATG[A/G]CCTCGCATCAAGGGCTGACTCGGCTCAATTCCAGTCGGATGAACTGGAGGTTCGTCATCC 233 3 0.8316159 1 rs131175700
ae1.8 ae1.8-128_T_F_1768567587 rs131175699 ss196416186 5 168463281 TOP [A/G] 73754362 TGAGACGACGGAGATGATACCATCCATCTTAAATTTTAGTTCCGAATGAT 36 0 0 diploid Zea mays Unknown 128 TOP ATCCATCTGTTGAGACGACGGAGATGATACCATCCATCTTAAATTTTAGTTCCGAATGAT[A/G]CCTTTTCAATTTTGACAAACAACATGACAACGTCGATTTAATATTTTGTTACTTCTATTG ATCCATCTGTTGAGACGACGGAGATGATACCATCCATCTTAAATTTTAGTTCCGAATGAT[A/G]CCTTTTCAATTTTGACAAACAACATGACAACGTCGATTTAATATTTTGTTACTTCTATTG 233 3 0.9600504 1 rs131175699
an1.3 an1.3-0_T_F_1605157644 rs131175334 ss196414714 1 241222672 TOP [A/C] 48609475 GGCTTCGAGATCGCCTTCCCTTCTCTCATCCAGACGGCTAGGGACCTGGG 1 0 0 diploid Zea mays Panzea 0 TOP GATGCCCATCGGCTTCGAGATCGCCTTCCCTTCTCTCATCCAGACGGCTAGGGACCTGGG[A/C]GTCGTCGACTTCCCGTACGGACACCCGKCSCTGCAGAGCATATACGCCAACAGGGARGTC GATGCCCATCGGCTTCGAGATCGCCTTCCCTTCTCTCATCCAGACGGCTAGGGACCTGGG[A/C]GTCGTCGACTTCCCGTACGGACACCCGKCSCTGCAGAGCATATACGCCAACAGGGARGTC 243 3 0.7794533 0.4524602 rs131175334
ba1.5 ba1.5-0_T_R_1605156958 rs131175538 ss196415563 3 183084768 TOP [A/G] 29780456 CGGTACGACCATGGGACGCGAGTGTCACCTCGTTGTCACCAACCACCGCC 1 0 0 diploid Zea mays Panzea 0 BOT AGGCCGCGCTGATGCAGCACGAGGAAGGATGYCATGCTGAGCTCGCCGCCTATTCCGCGG[T/C]GGCGGTGGTTGGTGACAACGAGGTGACACTCGCGTCCCATGGTCGTACCGGCGCATGCGA TCGCATGCGCCGGTACGACCATGGGACGCGAGTGTCACCTCGTTGTCACCAACCACCGCC[A/G]CCGCGGAATAGGCGGCGAGCTCAGCATGRCATCCTTCCTCGTGCTGCATCAGCGCGGCCT 233 3 0.8157448 0.4355737 rs131175538
ba1.6 ba1.6-0_T_F_1605157866 rs131175537 ss196415561 3 183084850 TOP [A/G] 60746419 GCGTCCCATGGTCGTACCGGCGCATGCGACGAGATGATGCAGCTCCAGGT 1 3 181362952 diploid Zea mays Panzea 0 TOP GGTGACACTCGCGTCCCATGGTCGTACCGGCGCATGCGACGAGATGATGCAGCTCCAGGT[A/G]GCGGCGGAGGAAGCTTTGAGTTAYGGTGTTGMTGCCCATCAGCCGTACGGGCTCGATCCC GGTGACACTCGCGTCCCATGGTCGTACCGGCGCATGCGACGAGATGATGCAGCTCCAGGT[A/G]GCGGCGGAGGAAGCTTTGAGTTAYGGTGTTGMTGCCCATCAGCCGTACGGGCTCGATCCC 233 3 0.8508628 0.5149003 rs131175537
ba1.7 ba1.7-0_T_R_1605157510 rs131175536 ss196415558 3 183085021 TOP [A/G] 74672433 TGCTACCTTAAGAAACTTCTACTACTACTCTAGTAAGAGCCGGGCAGACC 1 0 0 diploid Zea mays Panzea 0 BOT CTTCCTCGAGGAGCCTGCAGACGCATGCTACTCTGTGTGTGACCTCGACGACGGGGACAC[T/C]GGTCTGCCCGGCTCTTACTAGAGTAGTAGTAGAAGTTTCTTAAGGTAGCATCCCGTGTKT AMACACGGGATGCTACCTTAAGAAACTTCTACTACTACTCTAGTAAGAGCCGGGCAGACC[A/G]GTGTCCCCGTCGTCGAGGTCACACACAGAGTAGCATGCGTCTGCAGGCTCCTCGAGGAAG 233 3 0.8624125 0.5226186 rs131175536
bt-000002007 bt-000002007-0_B_R_1591116030 rs129711969 ss196417625 4 58956243 BOT [T/C] 28733489 CAACTTCCAACTGCAGCACAGTGAGAAGTGAAAGCATACCTGAAATCTGG 1 4 66290996 diploid Zea mays Public 0 TOP AGATATCGGTACCATTGCRGCATTTTATAATGCAAACTTGGGAATAACCAAGAAGCCAAT[A/G]CCAGATTTCAGGTATGCTTTCACTTCTCACTGTGCTGCAGTTGGAAGTTGCAACGCTGCA AGATATCGGTACCATTGCRGCATTTTATAATGCAAACTTGGGAATAACCAAGAAGCCAAT[A/G]CCAGATTTCAGGTATGCTTTCACTTCTCACTGTGCTGCAGTTGGAAGTTGCAACGCTGCA 233 3 0.4775205 0.6319712 rs129711969
bt2.2 bt2.2-0_B_F_1605157403 rs131175588 ss196415731 4 58959782 BOT [T/C] 23661481 GAGTGTCCATCTCGATGCCCGTGGCGCGGAGCCGGTCGTTCGTCTTCTCC 1 4 66287455 diploid Zea mays Panzea 0 BOT CGCAGCCGCGGAGTGTCCATCTCGATGCCCGTGGCGCGGAGCCGGTCGTTCGTCTTCTCC[T/C]CGCGCGCGGTGGCTGACTCCAAGAGCTCCCAGACCTGCCTGGACCCCGACGCCAGCACGG CCGTGCTGGCGTCGGGGTCCAGGCAGGTCTGGGAGCTCTTGGAGTCAGCCACCGCGCGCG[A/G]GGAGAAGACGAACGACCGGCTCCGCGCCACGGGCATCGAGATGGACACTCCGCGGCTGCG 233 3 0.7117587 0.4297523 rs131175588
bt2.4 bt2.4-0_B_F_1605158679 rs131175589 ss196415734 4 58958602 BOT [T/C] 25793419 CTCAAATGCAAAATCTGCCATTTCTATAACATGCACATTCCACACCATAT 1 4 66288635 diploid Zea mays Panzea 0 BOT TTCTGAWTNCCTCAAATGCAAAATCTGCCATTTCTATAACATGCACATTCCACACCATAT[T/C]CACATTTTNCTCATTGCATTTCTCGCTTCACACATCATTTTTTTCTCGAATACACACATC GATGTGTGTATTCGAGAAAAAAATGATGTGTGAAGCGAGAAATGCAATGAGNAAAATGTG[A/G]ATATGGTGTGGAATGTGCATGTTATAGAAATGGCAGATTTTGCATTTGAGGNAWTCAGAA 233 3 0.8664072 1 rs131175589
bt2.5 bt2.5-0_T_R_1605158440 rs131175590 ss196415736 4 58957188 TOP [A/G] 15808363 TTTACAAAATGATTGTCCACAAATGTAAATCAAGTTAGCTTGAAAGGAAA 1 4 66290049 diploid Zea mays Panzea 0 BOT TGAGTTTGCTGAGAAACCGAAAGGAGAGCAGTTGAAAGCAAYGATGGTACACATAATATG[T/C]TTTCCTTTCAAGCTAACTTGATTTACATTTGTGGACAATCATTTTGTAAACCTACAATAT ATATTGTAGGTTTACAAAATGATTGTCCACAAATGTAAATCAAGTTAGCTTGAAAGGAAA[A/G]CATATTATGTGTACCATCRTTGCTTTCAACTGCTCTCCTTTCGGTTTCTCAGCAAACTCA 233 3 0.8624125 0.5189453 rs131175590
bt2.8 bt2.8-0_T_F_1605156620 rs131175591 ss196415738 4 58956482 TOP [A/G] 62759380 CACAGATGTCATTATGCCATAAGTTGGTACCCTGACATTTCATTTCTGAA 1 4 66290755 diploid Zea mays Panzea 0 TOP AACCTTTTAACACAGATGTCATTATGCCATAAGTTGGTACCCTGACATTTCATTTCTGAA[A/G]AAGTGCATATCTGAAGTTTTATGTGCATCAAATGCTGCSTAGGAGCAGCTTACTARAAAG AACCTTTTAACACAGATGTCATTATGCCATAAGTTGGTACCCTGACATTTCATTTCTGAA[A/G]AAGTGCATATCTGAAGTTTTATGTGCATCAAATGCTGCSTAGGAGCAGCTTACTARAAAG 243 3 0.8460335 0.4513505 rs131175591
csu1138.3 csu1138.3-0_T_R_1605156320 rs131175304 ss196414598 1 120194613 TOP [A/G] 56627304 TGACCACCATTCAACTCCATCGATCAATGCTTGGCCGGAGGGTGGTAGAT 1 1 119018614 diploid Zea mays Panzea 0 BOT NAAACCACAACSTGAGCCTGAGTACCACCCMCCTACACCGACCTATGGATCACCGACTCC[T/C]ATCTACCACCCTCCGGCCAAGCATTGATCGATGGAGTTGAATGGTGGTCAGTGATCGACG CGTCGATCACTGACCACCATTCAACTCCATCGATCAATGCTTGGCCGGAGGGTGGTAGAT[A/G]GGAGTCGGTGATCCATAGGTCGGTGTAGGKGGGTGGTACTCAGGCTCASGTTGTGGTTTN 233 3 0.8156935 0.9357591 rs131175304
csu1138.4 csu1138.4-127_B_F_1605155327 rs131175303 ss196414596 1 120194710 BOT [T/C] 73750382 TCCGGCCAAGCATTGATCGATGGAGTTGAATGGTGGTCAGTGATCGACGT 36 0 0 diploid Zea mays Unknown 127 BOT TCTACCACCCTCCGGCCAAGCATTGATCGATGGAGTTGAATGGTGGTCAGTGATCGACGT[T/C]GCTAGCTANNNNAGAGTTGCATGTGTGGTCTAGCYARCGTGGTTTGCAGTCCYGCYTTTT AAAARGCRGGACTGCAAACCACGYTRGCTAGACCACACATGCAACTCTNNNNTAGCTAGC[A/G]ACGTCGATCACTGACCACCATTCAACTCCATCGATCAATGCTTGGCCGGAGGGTGGTAGA 243 3 0.7249529 0.5682456 rs131175303
csu1171.2 csu1171.2-128_T_F_1768567631 rs128381186 ss196414393 1 14638947 TOP [A/G] 29669497 CTATCAAAGGAATAAAGACCAGCCAAAGACCTCTAGCTGTAGCCGCATAA 36 0 0 diploid Zea mays Unknown 128 TOP KATTCTGCAGCTATCAAAGGAATAAAGACCAGCCAAAGACCTCTAGCTGTAGCCGCATAA[A/G]GAGCTGGACGTGTAATCATTTACTCTGTGCAAGTTTACCAGTGATGCGATCTGTATAGAT KATTCTGCAGCTATCAAAGGAATAAAGACCAGCCAAAGACCTCTAGCTGTAGCCGCATAA[A/G]GAGCTGGACGTGTAATCATTTACTCTGTGCAAGTTTACCAGTGATGCGATCTGTATAGAT 233 3 0.7432064 0.5089712 rs128381186
Fea2.2 Fea2.2-0_B_F_1605157523 rs131175610 ss196415811 4 133662781 BOT [T/C] 15722367 GCCCTGGCGTGTTTGGAGGATTGGACACCAAGGATGCACATAATTTGAAG 1 0 0 diploid Zea mays Panzea 0 BOT CTTGGTTGTAGCCCTGGCGTGTTTGGAGGATTGGACACCAAGGATGCACATAATTTGAAG[T/C]GCTGGTACTGTGAACCACTTCAGATGTAAATATTTTCTTTGGTTTTTAGTTCTGATCTAG CTAGATCAGAACTAAAAACCAAAGAAAATATTTACATCTGAAGTGGTTCACAGTACCAGC[A/G]CTTCAAATTATGTGCATCCTTGGTGTCCAATCCTCCAAACACGCCAGGGCTACAACCAAG 233 3 0.8631169 1 rs131175610
fea2.3 fea2.3-0_T_F_1605156066 rs129795307 ss196415814 4 133663063 TOP [A/G] 70667350 AAGAAACTTCGTGTTTCGGCCTGTGAGGGTTGAATATTAACAAGAGGGGA 1 0 0 diploid Zea mays Panzea 0 TOP CCTCTAATGCAAGAAACTTCGTGTTTCGGCCTGTGAGGGTTGAATATTAACAAGAGGGGA[A/G]ATTGCAAAATCAGGTTGTTTTGAAGTTCGAGCGACTCTGGTCTGCAGCTGATTAACAAGA CCTCTAATGCAAGAAACTTCGTGTTTCGGCCTGTGAGGGTTGAATATTAACAAGAGGGGA[A/G]ATTGCAAAATCAGGTTGTTTTGAAGTTCGAGCGACTCTGGTCTGCAGCTGATTAACAAGA 233 3 0.9330355 1 rs129795307
Fea2.5 Fea2.5-0_B_R_1605156695 rs131175611 ss196415816 4 133663191 BOT [T/C] 71608509 AATGATACATAGAAGCTAGTCATTGTGCTGATACAAAATGCACCAAGAGA 1 4 132734849 diploid Zea mays Panzea 0 TOP AATGGAAGGTAGCAATCACCGCGGTTGGYTTGGTGGCTGGCATGGAGAGAATGGATGGGT[A/G]TCTCTTGGTGCATTTTGTATCAGCACAATGACTAGCTTCTATGTATCATTAGCAACCTTA AATGGAAGGTAGCAATCACCGCGGTTGGYTTGGTGGCTGGCATGGAGAGAATGGATGGGT[A/G]TCTCTTGGTGCATTTTGTATCAGCACAATGACTAGCTTCTATGTATCATTAGCAACCTTA 233 3 0.9276718 0.8265173 rs131175611
lg2.12 lg2.12-0_T_R_1605158664 rs131175528 ss196415536 3 176805947 TOP [A/G] 60797300 ATCTGCATGCCAAAGAAAAAAGAGGCTCAGTACGGCGCGGGTGCACGGAC 1 3 175051925 diploid Zea mays Panzea 0 BOT TTCCGCCCGTCCGAGCTGCTCAAGGTANGCGGTCCTACTGCGTGCCATCGCCATGCCGTC[T/C]GTCCGTGCACCCGCGCCGTACTGAGCCTCTTTTTTCTTTGGCATGCAGATC GATCTGCATGCCAAAGAAAAAAGAGGCTCAGTACGGCGCGGGTGCACGGAC[A/G]GACGGCATGGCGATGGCACGCAGTAGGACCGCNTACCTTGAGCAGCTCGGACGGGCGGAA 243 3 0.7813367 0.6091152 rs131175528

Total number of rows: 56110

Table truncated, full table size 24870 Kbytes.




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