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Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg1117924359:

Variant ID: vg1117924359 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 17924359
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, G: 0.01, others allele: 0.00, population size: 88. )

Flanking Sequence (100 bp) in Reference Genome:


AATCTAATGCCACCAATTTAAGTAAAAATCGACGGTAAGATCATATAGTGCCATGTGGCAACCTAGGAGCGTTTGTAGATGTGCCACGTGGCGGCTTAGG[A/G]
GCGTTTTTAGGAAATTTAATGGACTTTTAGTATATAATAATAGATAGATAGATAGATAGATAGATTAGTACTCCCTCCGTCCCATAAAAAATCAACCAGT

Reverse complement sequence

ACTGGTTGATTTTTTATGGGACGGAGGGAGTACTAATCTATCTATCTATCTATCTATCTATTATTATATACTAAAAGTCCATTAAATTTCCTAAAAACGC[T/C]
CCTAAGCCGCCACGTGGCACATCTACAAACGCTCCTAGGTTGCCACATGGCACTATATGATCTTACCGTCGATTTTTACTTAAATTGGTGGCATTAGATT

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 58.10% 41.80% 0.06% 0.00% NA
All Indica  2759 76.00% 23.90% 0.07% 0.00% NA
All Japonica  1512 30.20% 69.80% 0.00% 0.00% NA
Aus  269 36.40% 63.20% 0.37% 0.00% NA
Indica I  595 69.40% 30.60% 0.00% 0.00% NA
Indica II  465 72.90% 27.10% 0.00% 0.00% NA
Indica III  913 79.60% 20.40% 0.00% 0.00% NA
Indica Intermediate  786 78.80% 21.00% 0.25% 0.00% NA
Temperate Japonica  767 5.30% 94.70% 0.00% 0.00% NA
Tropical Japonica  504 55.40% 44.60% 0.00% 0.00% NA
Japonica Intermediate  241 56.40% 43.60% 0.00% 0.00% NA
VI/Aromatic  96 42.70% 57.30% 0.00% 0.00% NA
Intermediate  90 61.10% 38.90% 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
vg1117924359 A -> G LOC_Os11g30770.1 upstream_gene_variant ; 2383.0bp to feature; MODIFIER silent_mutation Average:50.627; most accessible tissue: Zhenshan97 flower, score: 78.677 N N N N
vg1117924359 A -> G LOC_Os11g30760-LOC_Os11g30770 intergenic_region ; MODIFIER silent_mutation Average:50.627; most accessible tissue: Zhenshan97 flower, score: 78.677 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1117924359 1.19E-06 1.19E-06 mr1877 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
vg1117924359 NA 3.80E-06 mr1091_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
vg1117924359 NA 9.72E-07 mr1112_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
vg1117924359 9.74E-06 9.74E-06 mr1234_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