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Detailed information for vg0824847711:

Variant ID: vg0824847711 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 24847711
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.87, T: 0.13, others allele: 0.00, population size: 30. )

Flanking Sequence (100 bp) in Reference Genome:


ATTTCGAAATGCCTGAAACTTCTGTAGAAGTTTATTGGAATTTGATGTGCTCTTCAGCTTCTCGGGATGACTATTGCCTCGTTTTTTCATGAGCACACTT[C/T]
CTAAACTATTAAACTATATTAAGCTGTATATGTATTTTTTTATTGAATAGTTTCTTGAAAAATCAAATAAACTATGTTTATTGAATAGCCACTAAAAAGC

Reverse complement sequence

GCTTTTTAGTGGCTATTCAATAAACATAGTTTATTTGATTTTTCAAGAAACTATTCAATAAAAAAATACATATACAGCTTAATATAGTTTAATAGTTTAG[G/A]
AAGTGTGCTCATGAAAAAACGAGGCAATAGTCATCCCGAGAAGCTGAAGAGCACATCAAATTCCAATAAACTTCTACAGAAGTTTCAGGCATTTCGAAAT

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 69.10% 13.50% 12.42% 4.99% NA
All Indica  2759 56.00% 22.30% 14.17% 7.50% NA
All Japonica  1512 99.40% 0.40% 0.13% 0.07% NA
Aus  269 23.40% 0.00% 66.91% 9.67% NA
Indica I  595 60.80% 29.90% 9.24% 0.00% NA
Indica II  465 35.90% 52.70% 6.88% 4.52% NA
Indica III  913 62.00% 0.10% 22.45% 15.44% NA
Indica Intermediate  786 57.40% 24.30% 12.60% 5.73% NA
Temperate Japonica  767 99.20% 0.40% 0.26% 0.13% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 93.80% 0.00% 6.25% 0.00% NA
Intermediate  90 72.20% 16.70% 8.89% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0824847711 C -> T LOC_Os08g39320.1 upstream_gene_variant ; 3527.0bp to feature; MODIFIER silent_mutation Average:66.572; most accessible tissue: Callus, score: 84.714 N N N N
vg0824847711 C -> T LOC_Os08g39320-LOC_Os08g39330 intergenic_region ; MODIFIER silent_mutation Average:66.572; most accessible tissue: Callus, score: 84.714 N N N N
vg0824847711 C -> DEL N N silent_mutation Average:66.572; most accessible tissue: Callus, score: 84.714 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0824847711 NA 7.21E-06 mr1212 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
vg0824847711 NA 9.14E-09 mr1457 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
vg0824847711 5.50E-06 NA mr1699 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
vg0824847711 3.76E-07 7.13E-10 mr1699 Ind_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
vg0824847711 NA 3.81E-06 mr1727 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
vg0824847711 4.94E-06 NA mr1874 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
vg0824847711 NA 7.23E-09 mr1874 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
vg0824847711 3.24E-07 NA mr1699_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
vg0824847711 7.27E-07 3.84E-12 mr1699_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
vg0824847711 5.66E-06 NA mr1874_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
vg0824847711 5.27E-06 1.26E-12 mr1874_2 Ind_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