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Detailed information for vg0808122797:

Variant ID: vg0808122797 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 8122797
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:


CCTGTTTGGGGGGGGGGGTTGTTTGGTTAGGTGCCACACATTGCCACACCACATGTTAGGCATGCCATAAATTATTAGTTTAGCGTTTGGTTGCTTGTTT[C/T]
AGTTGTGGCAAGCCACACTTTCTTGTTCTATGGGCCTACATGTCATATACTCATTTTTTAGCCAAACAATGCCACACTTCTGGCCAACAAATTGTTGGCC

Reverse complement sequence

GGCCAACAATTTGTTGGCCAGAAGTGTGGCATTGTTTGGCTAAAAAATGAGTATATGACATGTAGGCCCATAGAACAAGAAAGTGTGGCTTGCCACAACT[G/A]
AAACAAGCAACCAAACGCTAAACTAATAATTTATGGCATGCCTAACATGTGGTGTGGCAATGTGTGGCACCTAACCAAACAACCCCCCCCCCCAAACAGG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 90.30% 9.70% 0.00% 0.00% NA
All Indica  2759 99.80% 0.20% 0.00% 0.00% NA
All Japonica  1512 70.50% 29.50% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 99.80% 0.20% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.10% 0.00% 0.00% NA
Temperate Japonica  767 90.90% 9.10% 0.00% 0.00% NA
Tropical Japonica  504 32.70% 67.30% 0.00% 0.00% NA
Japonica Intermediate  241 84.60% 15.40% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 92.20% 7.80% 0.00% 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
vg0808122797 C -> T LOC_Os08g13660.1 upstream_gene_variant ; 2227.0bp to feature; MODIFIER silent_mutation Average:51.903; most accessible tissue: Zhenshan97 panicle, score: 59.59 N N N N
vg0808122797 C -> T LOC_Os08g13650.1 intron_variant ; MODIFIER silent_mutation Average:51.903; most accessible tissue: Zhenshan97 panicle, score: 59.59 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0808122797 1.34E-06 1.34E-06 mr1146 Jap_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
vg0808122797 NA 1.22E-06 mr1248 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
vg0808122797 NA 3.55E-08 mr1668 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