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Detailed information for vg0817551415:

Variant ID: vg0817551415 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 17551415
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.93, A: 0.07, others allele: 0.00, population size: 204. )

Flanking Sequence (100 bp) in Reference Genome:


TGTAGTACAAATTTATGGAGCAGCTCTGCTAACTCCGCTCCAAAAAATAAAGAAATATGTATCGATTGGCACAACTCCAGCTTTAAATAAGTTGGAGTTT[G/A]
GAGCTAGAACTGTGCCAAACGGGTAGAAAAAGAATAGTTGTAACAACTCAGTTTTTTCTTACTAAGTGGAAAAATGGAATTCTTGTTGCTTTGAACGCTC

Reverse complement sequence

GAGCGTTCAAAGCAACAAGAATTCCATTTTTCCACTTAGTAAGAAAAAACTGAGTTGTTACAACTATTCTTTTTCTACCCGTTTGGCACAGTTCTAGCTC[C/T]
AAACTCCAACTTATTTAAAGCTGGAGTTGTGCCAATCGATACATATTTCTTTATTTTTTGGAGCGGAGTTAGCAGAGCTGCTCCATAAATTTGTACTACA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 92.80% 7.00% 0.17% 0.00% NA
All Indica  2759 97.60% 2.20% 0.22% 0.00% NA
All Japonica  1512 85.90% 14.10% 0.00% 0.00% NA
Aus  269 84.00% 16.00% 0.00% 0.00% NA
Indica I  595 97.30% 2.70% 0.00% 0.00% NA
Indica II  465 97.80% 0.90% 1.29% 0.00% NA
Indica III  913 98.10% 1.90% 0.00% 0.00% NA
Indica Intermediate  786 96.90% 3.10% 0.00% 0.00% NA
Temperate Japonica  767 99.30% 0.70% 0.00% 0.00% NA
Tropical Japonica  504 63.50% 36.50% 0.00% 0.00% NA
Japonica Intermediate  241 90.00% 10.00% 0.00% 0.00% NA
VI/Aromatic  96 92.70% 7.30% 0.00% 0.00% NA
Intermediate  90 90.00% 7.80% 2.22% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0817551415 G -> A LOC_Os08g28700-LOC_Os08g28710 intergenic_region ; MODIFIER silent_mutation Average:51.926; most accessible tissue: Zhenshan97 panicle, score: 68.538 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0817551415 2.10E-06 6.90E-07 mr1040 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0817551415 1.51E-06 9.79E-09 mr1836 All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0817551415 NA 3.72E-06 mr1852 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0817551415 5.81E-06 NA mr1836_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0817551415 NA 8.43E-06 mr1836_2 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251