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Platform GPL21735 Query DataSets for GPL21735
Status Public on Apr 15, 2016
Title Affymetrix Axiom® Turkey Genotyping Array
Technology type in situ oligonucleotide
Distribution custom-commercial
Organism Meleagris gallopavo
Manufacturer Affymetrix
Manufacture protocol see manufacturer's web site
Catalog number 550538
 
Description The Axiom®Turkey Genotyping Array interrogates 643,845 probesets on the array, covering 643,845 SNPs. The array development was led by Dr. Julie Long of the USDA-ARS Beltsville Agricultural Research Center under a public-private partnership with Hendrix Genetics, Aviagen, and Affymetrix. The Turkey Genome Sequencing Consortium led the efforts to sequence the turkey genome. The SNP marker discovery effort was led by Prof. Martien Groenen of the Animal Breeding and Genomics Centre at Wageningen University in the Netherlands, and was funded by USDA’s National Institute of Food and Agriculture. The SNP markers on the turkey array were selected by Dr. Curt Van Tassell of the USDA-ARS Beltsville Agricultural Research Center.
Reference genome version for which chromosome and position coordinates are given: UMD 5.0
 
Contributor(s) Long J, Groenen M, Van Tassell C
Submission date Apr 14, 2016
Last update date Apr 15, 2016
Contact name Julie A Long
E-mail(s) julie.long@ars.usda.gov
Phone 3015048580
Organization name USDA/ARS
Street address Powder Mill Road
City Beltsville
State/province MD
ZIP/Postal code 20705
Country USA
 

Data table header descriptions
ID Affymetrix probe set ID used in Affymetrix annotation file
Affy SNP_ID Affymetrix SNP ID used in Affymetrix annotation file
CUST_ID Customer ID used in Affymetrix annotation file
CHROMOSOME Chromosomal location of the SNP (chromosomes 1 to 10; UNK: SNP not anchored to UMD5.0)
PHYSICAL_POSITION Physical position in bp
TILE_STRAND Strand used for tiling the probe (f: forward, r: reverse)
ALLELES_F Forward alleles
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

Data table
ID Affy SNP_ID CUST_ID CHROMOSOME PHYSICAL_POSITION TILE_STRAND ALLELES_F SEQUENCE FLANKING_SEQUENCE ALLELE_A ALLELE_B
AX-115920537 Affx-114401279 UMD5_1_125277563 1 125277563 f C/T AAGCAACAGTGATAGGATGAGTGGCAATAG TTCCCAAGCAACAGTGATAGGATGAGTGGCAATAG[C/T]CTCATGTTGTGCCGGAAGAGGTTCAGATTGGATAT T C
AX-115920538 Affx-114401314 UMD5_1_90437181 1 90437181 f C/T GACTAACATTTGTCAGATATCAGGAGTTCT TGTATGACTAACATTTGTCAGATATCAGGAGTTCT[C/T]GCACACTATAAGTGAAAAGTGCTTGTAATAATATC T C
AX-115920539 Affx-114401420 UMD5_1_155423047 1 155423047 f A/G TGAAGTCCTGTATCTGCATCTATGATCTTT TCCTCTGAAGTCCTGTATCTGCATCTATGATCTTT[A/G]GTGAATTTGAAAAACACAGCAGGGATCTTTCCAGA A G
AX-115920540 Affx-114401480 UMD5_1_142615455 1 142615455 f A/G ACAGATTTCTTTTCTTTTTTTCTCTTGTAC GTTAGACAGATTTCTTTTCTTTTTTTCTCTTGTAC[A/G]CCATCCAGAAATAATCAAAGCAGGTTAGAATGGGA A G
AX-115920541 Affx-114401488 UMD5_1_66666404 1 66666404 f A/G ACTTTACTCGGGAATCTTAGGAAAATATAA ATGGCACTTTACTCGGGAATCTTAGGAAAATATAA[A/G]TTAGAATGACTTCAAATCAATCTGCTGCCTGCCAG A G
AX-115920542 Affx-114401549 UMD5_3_19859579 3 19859579 f A/G ATGTTTTTCAATTAAAAGAGGAGAGATTTA GGGGAATGTTTTTCAATTAAAAGAGGAGAGATTTA[A/G]GTTTAGAAATTTTTTTACTCAAGGGAGTGGTGTGA A G
AX-115920543 Affx-114401566 UMD5_1_157808251 1 157808251 f C/G GACATACATATTGTATTTTCAGTCTTCTGT CATAAGACATACATATTGTATTTTCAGTCTTCTGT[C/G]ACACTGAGTATATCCAACTACCTCTTATTGTTAAT C G
AX-115920544 Affx-114401571 UMD5_1_109965536 1 109965536 f C/T CTCATCCCCCTCCGTTGTGCTTTTGTCAGT CTTCTCTCATCCCCCTCCGTTGTGCTTTTGTCAGT[C/T]ACTCCTTTTCTTCCCAGCTCTATTTTTCTATTTCC T C
AX-115920545 Affx-114401608 UMD5_1_64167861 1 64167861 f A/G CTTTCAAAACACGTATGTGAAGGTGCTCTT TTTGTCTTTCAAAACACGTATGTGAAGGTGCTCTT[A/G]CACTGCAACATAATTTAAATTAATGTAAATGACAC A G
AX-115920546 Affx-114401684 UMD5_1_108011217 1 108011217 f A/G GATGAAAAGAGAGGGGAAGTACATCCAGAT TAAGAGATGAAAAGAGAGGGGAAGTACATCCAGAT[A/G]TGGTGCATCACCAGCACTTCTCAAGGAAATCTGAG A G
AX-115920547 Affx-114401698 UMD5_4_59047212 4 59047212 f A/G GCAATTAAACATGAACTTAACTCACCCACC CAGTAGCAATTAAACATGAACTTAACTCACCCACC[A/G]AAAGAGCAGTTGTCAGAAAATAATAAATTTTTATT A G
AX-115920548 Affx-114401801 UMD5_1_172881575 1 172881575 f A/G GCCTCCCAGTGTTTTTAGGTCTAGTGTTTG TTAAGGCCTCCCAGTGTTTTTAGGTCTAGTGTTTG[A/G]GTCCAGACTTGGTGTAGTTTATAGGATGTCTGCCA A G
AX-115920549 Affx-114401835 UMD5_1_119275136 1 119275136 f C/G AGTGAATGAAAAGAATATAAACATGGCTTT GTTCGAGTGAATGAAAAGAATATAAACATGGCTTT[C/G]AATTTGTATTCTGTTATCCATCATGTATTACCATA C G
AX-115920550 Affx-114401836 UMD5_1_42137594 1 42137594 f C/T TTAGAGAATCCAAAGCAGACAAGGTAAGGA AAAGTTTAGAGAATCCAAAGCAGACAAGGTAAGGA[C/T]AACGAAAAGTGCAGAGAAATGTGTTCTTCTGTCTT T C
AX-115920551 Affx-114401848 UMD5_22_2616070 22 2616070 f C/T GTTTGGGTCTCATCTTGCTGATTTGAGTCA TTAAGGTTTGGGTCTCATCTTGCTGATTTGAGTCA[C/T]GTGAGTTGTGATAATCCCTCACAGGGCCCCTGGTC T C
AX-115920552 Affx-114402135 UMD5_1_131788643 1 131788643 f A/G TTTGAGGCAGTATGCACGCACGCATTCCGT TTTTTTTTGAGGCAGTATGCACGCACGCATTCCGT[A/G]TGTATACAATAAAGAAAGGGAACAAATTCAAGTCA A G
AX-115920553 Affx-114402182 UMD5_1_57007200 1 57007200 f C/T ATTAAAAATAAGCCTAATAAACTAACCCCC TTTATATTAAAAATAAGCCTAATAAACTAACCCCC[C/T]TTTTTGTTTGCAGTAGGAAGTCTGTATTATAAAGA T C
AX-115920554 Affx-114402212 UMD5_1_52772681 1 52772681 f A/T TAGGGAGATGATTTTCCTGAAGAGATTCTG CTCTGTAGGGAGATGATTTTCCTGAAGAGATTCTG[A/T]TTAATAGCTTGTGGCTTCGTTCTGAGTAGAGGAGT A T
AX-115920555 Affx-114402225 UMD5_3_3758732 3 3758732 f G/T CCTGACCTGTCCCAGCTCTATCCTGCTCTA CATAACCTGACCTGTCCCAGCTCTATCCTGCTCTA[G/T]CATTATTCATTCCCCCACAGTCTAACCTACATGAA T G
AX-115920556 Affx-114402228 UMD5_1_28382515 1 28382515 f A/G ATGTGCAGGATGTTCCCTGTATATTAAAAA CATCCATGTGCAGGATGTTCCCTGTATATTAAAAA[A/G]TCTCTGTAGGAAATGTGTTGTGCACAGTGGTTCTT A G

Total number of rows: 643845

Table truncated, full table size 110250 Kbytes.




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