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Detailed information for vg0810945945:

Variant ID: vg0810945945 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 10945945
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, T: 0.00, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:


ACTAGTGTAAATAAGATCTCTTGATAGTATTGTCCCCATTTTGGCTGATATGACGCCTACGTGGCTCTTTAGACTAAATCTTTGTCCCACGCGCATTGAC[G/T]
TGACGCTTACGTGGCAATTTGATCCGAAAAAAATAAAAGGAGAAAAATTAGAAAAAAATATGCGGGGCCATATGTCTAATGTCTACAAGAAGATAAAAAA

Reverse complement sequence

TTTTTTATCTTCTTGTAGACATTAGACATATGGCCCCGCATATTTTTTTCTAATTTTTCTCCTTTTATTTTTTTCGGATCAAATTGCCACGTAAGCGTCA[C/A]
GTCAATGCGCGTGGGACAAAGATTTAGTCTAAAGAGCCACGTAGGCGTCATATCAGCCAAAATGGGGACAATACTATCAAGAGATCTTATTTACACTAGT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 94.80% 5.20% 0.06% 0.00% NA
All Indica  2759 98.90% 1.10% 0.00% 0.00% NA
All Japonica  1512 89.70% 10.30% 0.00% 0.00% NA
Aus  269 82.20% 17.10% 0.74% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 99.30% 0.70% 0.00% 0.00% NA
Indica Intermediate  786 97.10% 2.90% 0.00% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 73.00% 27.00% 0.00% 0.00% NA
Japonica Intermediate  241 92.90% 7.10% 0.00% 0.00% NA
VI/Aromatic  96 93.80% 6.20% 0.00% 0.00% NA
Intermediate  90 91.10% 7.80% 1.11% 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
vg0810945945 G -> T LOC_Os08g17850.1 upstream_gene_variant ; 4173.0bp to feature; MODIFIER silent_mutation Average:61.154; most accessible tissue: Zhenshan97 young leaf, score: 75.751 N N N N
vg0810945945 G -> T LOC_Os08g17830.1 downstream_gene_variant ; 812.0bp to feature; MODIFIER silent_mutation Average:61.154; most accessible tissue: Zhenshan97 young leaf, score: 75.751 N N N N
vg0810945945 G -> T LOC_Os08g17830-LOC_Os08g17850 intergenic_region ; MODIFIER silent_mutation Average:61.154; most accessible tissue: Zhenshan97 young leaf, score: 75.751 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0810945945 7.02E-07 NA mr1134 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
vg0810945945 NA 9.03E-06 mr1134 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
vg0810945945 2.91E-07 NA mr1504 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
vg0810945945 NA 1.15E-06 mr1583 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
vg0810945945 1.22E-07 3.29E-08 mr1835 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