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Detailed information for vg0808046261:

Variant ID: vg0808046261 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 8046261
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.93, T: 0.06, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:


GCTGGCAAAAAATAAACCTGGACTAAAGATGATCTTTAGATCATAAAGTTCTGTTGCGCTTTTTAACCGGGACTAAAAATGATCTTTAGTCCGGCCGGTT[C/T]
CTAACTTCCTATTCGAAACAGGACTATATCATTTTTGCATGACCCGGCGAAAATCACTTCTCCAGTAGTGAAAGAAACCGGTAAAACTTTTCTCCCCATC

Reverse complement sequence

GATGGGGAGAAAAGTTTTACCGGTTTCTTTCACTACTGGAGAAGTGATTTTCGCCGGGTCATGCAAAAATGATATAGTCCTGTTTCGAATAGGAAGTTAG[G/A]
AACCGGCCGGACTAAAGATCATTTTTAGTCCCGGTTAAAAAGCGCAACAGAACTTTATGATCTAAAGATCATCTTTAGTCCAGGTTTATTTTTTGCCAGC

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 52.60% 45.20% 0.08% 2.14% NA
All Indica  2759 87.00% 12.90% 0.11% 0.00% NA
All Japonica  1512 2.00% 91.30% 0.07% 6.61% NA
Aus  269 4.10% 95.90% 0.00% 0.00% NA
Indica I  595 92.80% 7.20% 0.00% 0.00% NA
Indica II  465 80.60% 19.40% 0.00% 0.00% NA
Indica III  913 86.50% 13.50% 0.00% 0.00% NA
Indica Intermediate  786 86.80% 12.80% 0.38% 0.00% NA
Temperate Japonica  767 2.20% 94.80% 0.00% 3.00% NA
Tropical Japonica  504 1.40% 95.80% 0.00% 2.78% NA
Japonica Intermediate  241 2.50% 71.00% 0.41% 26.14% NA
VI/Aromatic  96 3.10% 96.90% 0.00% 0.00% NA
Intermediate  90 47.80% 51.10% 0.00% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0808046261 C -> T LOC_Os08g13540.1 upstream_gene_variant ; 3104.0bp to feature; MODIFIER silent_mutation Average:46.708; most accessible tissue: Callus, score: 75.668 N N N N
vg0808046261 C -> T LOC_Os08g13530.1 downstream_gene_variant ; 700.0bp to feature; MODIFIER silent_mutation Average:46.708; most accessible tissue: Callus, score: 75.668 N N N N
vg0808046261 C -> T LOC_Os08g13520-LOC_Os08g13530 intergenic_region ; MODIFIER silent_mutation Average:46.708; most accessible tissue: Callus, score: 75.668 N N N N
vg0808046261 C -> DEL N N silent_mutation Average:46.708; most accessible tissue: Callus, score: 75.668 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0808046261 NA 3.07E-06 mr1317 Ind_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
vg0808046261 NA 9.84E-08 mr1610 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
vg0808046261 NA 3.92E-16 mr1914 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
vg0808046261 NA 2.17E-07 mr1855_2 Ind_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
vg0808046261 NA 1.42E-06 mr1914_2 Ind_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