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Platform GPL18778 Query DataSets for GPL18778
Status Public on Jun 11, 2014
Title [Axiom_Maize600] Affymetrix Axiom® Maize Genotyping Array
Technology type in situ oligonucleotide
Distribution commercial
Organism Zea mays
Manufacturer Affymetrix
Manufacture protocol see manufacturer's web site
Catalog number 550494
 
Description The Axiom® Maize Genotyping Array interrogates 616,201 polymorphic variants (609,442 SNPs and 6,759 indels) to represent the global diversity in the maize genome. Development of the array is described in the following publication:
Unterseer S, Bauer E, Haberer G, Seidel M, Knaak C, Ouzunova M, Meitinger T, Strom TM, Fries R, Pausch H, Bertani C, Davassi A, Mayer KFX, Schön C-C (2014) A powerful tool for genome analysis in maize: development and evaluation of the high density 600 k SNP genotyping array. BMC Genomics 15:823, PMID: 25266061
The array was designed by the AgroClustER Synbreed (funded by the German Ministry of Education and Research, BMBF) through a collaboration led by Prof. Dr. Chris-Carolin Schön, Dr. Eva Bauer, and Sandra Unterseer (Technische Universität München, Germany), and Dr. Georg Haberer and Michael Seidel (Helmholtz Zentrum München, Germany) through Affymetrix® Expert Design Program.
 
Web link http://www.affymetrix.com/catalog/prod820010/AFFY/Axiom%26%23174%3B-Maize-Genotyping-Array#1_1
Contributor(s) Bauer E, Unterseer S, Haberer G, Seidel M, Knaak C, Ouzunova M, Meitinger T, Strom TM, Fries R, Pausch H, Bertani C, Davassi A, Mayer KF, Schön C
Citation(s) 25266061
Submission date Jun 11, 2014
Last update date Oct 01, 2014
Organization Affymetrix, Inc.
E-mail(s) geo@ncbi.nlm.nih.gov, support@affymetrix.com
Phone 888-362-2447
URL http://www.affymetrix.com/index.affx
Street address
City Santa Clara
State/province CA
ZIP/Postal code 95051
Country USA
 

Data table header descriptions
ID Unique identifier (identical with Affymetrix probe set ID)
probe_set_ID Affymetrix probe set ID used in Affymetrix annotation file
Affy_SNP_ID Affymetrix SNP ID used in Affymetrix annotation file
cust_ID "Custom SNP ID used by the developers of the array or taken from the original ID used for 45,655 SNPs included from the Illumina MaizeSNP50 BeadChip (NCBI GEO accession number GPL17677)"
organism Organism
chromosome Chromosomal location of the SNP (chromosomes 1 to 10; UNK: SNP not anchored to B73 RefGen_v2)
physical_position Physical position in bp
genome_acc Reference genome version for which chromosome and position coordinates are given
tile_strand "Strand used for tiling the probe (f: forward, r: reverse)"
alleles_f Forward alleles
ligation_bases Ligation bases
SEQUENCE Probe sequence
flanking_sequence Flanking sequence of the SNP (or indel) on the plus (+) strand of the reference sequence
allele_A Allele A
allele_B Allele B
SPOT_ID

Data table
ID probe_set_ID Affy_SNP_ID cust_ID organism chromosome physical_position genome_acc tile_strand alleles_f ligation_bases SEQUENCE flanking_sequence allele_A allele_B SPOT_ID
AX-90525723 AX-90525723 Affx-90758874 PHM1506.18 Zea mays 10 148972870 B73 RefGen_v2 f C/T C/T ATCGGGGCCTAAGGTAGACGCCAGTGGTTC ACACAATCGGGGCCTAAGGTAGACGCCAGTGGTTC[C/T]GAGAACGGGAGAGACGTGCTTCTGTTGATGTACTG T C B73 RefGen_v2; chr 10 (148972870)
AX-90525726 AX-90525726 Affx-90293863 PHM15331.16 Zea mays 10 10882576 B73 RefGen_v2 f C/T C/T AACGACGCTCTTCCGCACGTCCAACCGCAG AGGCCAACGACGCTCTTCCGCACGTCCAACCGCAG[C/T]GAGCGCCTGAAGACGCGGCCAAAGCTGGGGATCAG T C B73 RefGen_v2; chr 10 (10882576)
AX-90525729 AX-90525729 Affx-90864597 PHM1626.34 Zea mays 3 156482775 B73 RefGen_v2 f C/T C/T TTTCGAGTTCATCTTCTGGACCTCCTCCTT GCTGATTTCGAGTTCATCTTCTGGACCTCCTCCTT[C/T]GTGTAGATGTAGATCTTGCGCACTATGCTGCAGAA T C B73 RefGen_v2; chr 3 (156482775)
AX-90525738 AX-90525738 Affx-90967383 PHM3075.15 Zea mays 3 191612649 B73 RefGen_v2 f C/T C/T CACAGTTCCGGCAATGTTCCGATGAGAAAA AACCTCACAGTTCCGGCAATGTTCCGATGAGAAAA[C/T]CAGTCAACTCGCCGAGCCAAAGATAAGAAAGAAAG T C B73 RefGen_v2; chr 3 (191612649)
AX-90525741 AX-90525741 Affx-90601730 PHM3309.8 Zea mays 2 5839907 B73 RefGen_v2 f C/T C/T CGTTTTGAAACGACTGTAAATCCCTCTGTA TTCGACGTTTTGAAACGACTGTAAATCCCTCTGTA[C/T]CCTTCAGGCCCTTGGGAACCTCCATGGATTTCTCT T C B73 RefGen_v2; chr 2 (5839907)
AX-90525746 AX-90525746 Affx-90194631 PHM3714.12 Zea mays 5 2926821 B73 RefGen_v2 f A/G A/G GAAGAGTGTGCTCAGAGCAGAGAAGATAGG TCAGAGAAGAGTGTGCTCAGAGCAGAGAAGATAGG[A/G]CTATCGGAATGGTCATCTTCATTGTGGTTAGTACT A G B73 RefGen_v2; chr 5 (2926821)
AX-90525748 AX-90525748 Affx-91054640 PHM4185.17 Zea mays 1 83780916 B73 RefGen_v2 f A/G A/G AAGCATCAGCATTTTGAGGCAACATGAGCT ACAAGAAGCATCAGCATTTTGAGGCAACATGAGCT[A/G]AAACAAAAGCTTTCCAGTTTATGGGTCAGAATTCG A G B73 RefGen_v2; chr 1 (83780916)
AX-90525756 AX-90525756 Affx-90294728 PHM5098.25 Zea mays 1 67646946 B73 RefGen_v2 f C/T C/T TTTGCGTTTCCAGAGCCATGCGGTGCTTGC ACTGATTTGCGTTTCCAGAGCCATGCGGTGCTTGC[C/T]CTCCAGGAGGCTGCTGAGGCATACCTTGTTGGCCT T C B73 RefGen_v2; chr 1 (67646946)
AX-90525763 AX-90525763 Affx-90315003 PHM6795.5 Zea mays 5 44407599 B73 RefGen_v2 f C/T C/T GCAGGGCCATTATACCAGAGGATACGGCGA CGCAAGCAGGGCCATTATACCAGAGGATACGGCGA[C/T]TAAAGTGTCAGCCTCTCCAACGAAACCACAGCATC T C B73 RefGen_v2; chr 5 (44407599)
AX-90525768 AX-90525768 Affx-91218396 PHM9266.23 Zea mays 10 80719215 B73 RefGen_v2 f C/T C/T ATACTAATGGAACTTTGCGCAAAGAAGAAG ACAGAATACTAATGGAACTTTGCGCAAAGAAGAAG[C/T]AAATGAGGATGCCAAATGGTAAGTACTTATCTAAG T C B73 RefGen_v2; chr 10 (80719215)
AX-90525769 AX-90525769 Affx-91102582 PHM9266.25 Zea mays 10 80719268 B73 RefGen_v2 f A/G A/G GTACTTATCTAAGTGCTTTGTGAGTTGTTT GGTAAGTACTTATCTAAGTGCTTTGTGAGTTGTTT[A/G]CCATTGGAATTTAACCTTGCCAGATACACAAAATA A G B73 RefGen_v2; chr 10 (80719268)
AX-90525770 AX-90525770 Affx-90145683 PHM9374.5 Zea mays 9 17750933 B73 RefGen_v2 f C/T C/T TATTGCAGCATGCCAGCATTTACATGCTAA GATAGTATTGCAGCATGCCAGCATTTACATGCTAA[C/T]GGGTTCAGTTTATTCCCAGGGAAAGTAGTGGAGTA T C B73 RefGen_v2; chr 9 (17750933)
AX-90525773 AX-90525773 Affx-90559611 PHM9914.11 Zea mays 3 161257992 B73 RefGen_v2 f A/G A/G CGACACCGATCATGAGGAGATGCTATCTGG CATGGCGACACCGATCATGAGGAGATGCTATCTGG[A/G]TTACACAAGACTGTGATCGTCCGGGGTGTCACCGA A G B73 RefGen_v2; chr 3 (161257992)
AX-90525774 AX-90525774 Affx-91268521 PUT-163a-101381786-1 Zea mays 8 138143276 B73 RefGen_v2 f C/T C/T ACGCTGCTGGCGTCGATCCTCCTCTCTGCT ATAAGACGCTGCTGGCGTCGATCCTCCTCTCTGCT[C/T]GCCGCACTCAGGCGTCCACGACCTCGTCGTCCTTG T C B73 RefGen_v2; chr 8 (138143276)
AX-90525776 AX-90525776 Affx-90266102 PUT-163a-101387821-12 Zea mays 3 216345579 B73 RefGen_v2 f A/G A/G CTGTTGATTTTATCACGAATTAATACTACT TCGCCCTGTTGATTTTATCACGAATTAATACTACT[A/G]TTTCCAGGTTACTAGCTCTCGAACTCATGGCTTTC A G B73 RefGen_v2; chr 3 (216345579)
AX-90525777 AX-90525777 Affx-91258543 PUT-163a-101389210-15 Zea mays 8 152766279 B73 RefGen_v2 f A/C A/C ATTTCTGTCAGACAGTAAATATGATGCTCC GTGGAATTTCTGTCAGACAGTAAATATGATGCTCC[A/C]CTGAAGCTAAAGAAGAAGAGCAAAAAGAAGAAAAT A C B73 RefGen_v2; chr 8 (152766279)
AX-90525783 AX-90525783 Affx-90447105 PUT-163a-110194326-44 Zea mays 2 236046926 B73 RefGen_v2 f A/G A/G AGAGTCTATTTCCAGATATTATCGTGCACA TGTCTAGAGTCTATTTCCAGATATTATCGTGCACA[A/G]TACAAACCAATTTCAGCAAAACGTCACACAGGGAG A G B73 RefGen_v2; chr 2 (236046926)
AX-90525786 AX-90525786 Affx-90630858 PUT-163a-110204885-63 Zea mays 3 31898366 B73 RefGen_v2 f A/C A/C CACGCTTAGTCCAACAACAATGGGTTCTTA CTCGTCACGCTTAGTCCAACAACAATGGGTTCTTA[A/C]TTCTTACAAATATATACCAACGCTGCCACTCAGTG A C B73 RefGen_v2; chr 3 (31898366)
AX-90525793 AX-90525793 Affx-91222816 PUT-163a-110481372-81 Zea mays 5 162680869 B73 RefGen_v2 f A/G A/G CCTTATCTCTACAGAAAACGTGCTTGCGGC AAACTCCTTATCTCTACAGAAAACGTGCTTGCGGC[A/G]TATGTATGTGCCACGTTTACCGATTCTTCTTCGTT A G B73 RefGen_v2; chr 5 (162680869)
AX-90525795 AX-90525795 Affx-90718587 PUT-163a-110504512-88 Zea mays 2 207841753 B73 RefGen_v2 f C/T C/T GCAATCTTCATGATTACGGTAATATGTGCT CTGAAGCAATCTTCATGATTACGGTAATATGTGCT[C/T]CATGGAGGTATGACCATCAGCAGAGACACTCATGG T C B73 RefGen_v2; chr 2 (207841753)

Total number of rows: 616201

Table truncated, full table size 140988 Kbytes.




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