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Detailed information for vg0810050412:

Variant ID: vg0810050412 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 10050412
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.60, G: 0.40, others allele: 0.00, population size: 92. )

Flanking Sequence (100 bp) in Reference Genome:


TTTTGCTTTGGCTTATTAGGCCAACCGATAAGGCTCTTAAACTACCAATAAGTTGGGTACTACTTTTTCAGATGTTCTTAGTTTAGTGTAGCTTTATGGT[A/G]
TGGTTTTTTCTGTGTATTGTTTAACCTATTTTTTCTCGGGTGTTCCTTTTTGTCCTAGAATTACTATACAATTGTCAACAATTTTTCTCCAAAAAGCCTT

Reverse complement sequence

AAGGCTTTTTGGAGAAAAATTGTTGACAATTGTATAGTAATTCTAGGACAAAAAGGAACACCCGAGAAAAAATAGGTTAAACAATACACAGAAAAAACCA[T/C]
ACCATAAAGCTACACTAAACTAAGAACATCTGAAAAAGTAGTACCCAACTTATTGGTAGTTTAAGAGCCTTATCGGTTGGCCTAATAAGCCAAAGCAAAA

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 57.40% 16.10% 0.15% 26.36% NA
All Indica  2759 76.40% 4.70% 0.18% 18.74% NA
All Japonica  1512 25.60% 33.50% 0.13% 40.81% NA
Aus  269 61.30% 36.80% 0.00% 1.86% NA
Indica I  595 86.60% 9.60% 0.17% 3.70% NA
Indica II  465 75.90% 2.60% 0.22% 21.29% NA
Indica III  913 70.30% 1.10% 0.00% 28.59% NA
Indica Intermediate  786 76.00% 6.50% 0.38% 17.18% NA
Temperate Japonica  767 36.10% 54.60% 0.26% 9.00% NA
Tropical Japonica  504 8.10% 9.50% 0.00% 82.34% NA
Japonica Intermediate  241 28.60% 16.20% 0.00% 55.19% NA
VI/Aromatic  96 11.50% 2.10% 0.00% 86.46% NA
Intermediate  90 47.80% 25.60% 0.00% 26.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0810050412 A -> G LOC_Os08g16430.1 upstream_gene_variant ; 1113.0bp to feature; MODIFIER silent_mutation Average:40.857; most accessible tissue: Zhenshan97 young leaf, score: 48.658 N N N N
vg0810050412 A -> G LOC_Os08g16420-LOC_Os08g16430 intergenic_region ; MODIFIER silent_mutation Average:40.857; most accessible tissue: Zhenshan97 young leaf, score: 48.658 N N N N
vg0810050412 A -> DEL N N silent_mutation Average:40.857; most accessible tissue: Zhenshan97 young leaf, score: 48.658 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0810050412 NA 7.55E-06 mr1069 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
vg0810050412 NA 1.80E-06 mr1164 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
vg0810050412 NA 4.88E-07 mr1617 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
vg0810050412 NA 5.51E-08 mr1627 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
vg0810050412 NA 7.54E-06 mr1057_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
vg0810050412 NA 1.32E-06 mr1164_2 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
vg0810050412 NA 3.41E-07 mr1627_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