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

Detailed information for vg0318167000:

Variant ID: vg0318167000 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 18167000
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AACTTATCCCGTGCGCCTCCTCCTCCTCCTCGATGTTGCGCGCACGCCTCATCCTCTCCGCGCATGCGGATCTTTTTTTTCCTGGTTGTTTAACAACCGG[A/G]
ACTAGAAATAGCTCTTTAGTCCAACCGGGATTAAAGGTAAAGGAGGGGTCTGACACCGCCTACCTTTTTTGAACTAGGATTAAAGATTAAAAAGTAGCTC

Reverse complement sequence

GAGCTACTTTTTAATCTTTAATCCTAGTTCAAAAAAGGTAGGCGGTGTCAGACCCCTCCTTTACCTTTAATCCCGGTTGGACTAAAGAGCTATTTCTAGT[T/C]
CCGGTTGTTAAACAACCAGGAAAAAAAAGATCCGCATGCGCGGAGAGGATGAGGCGTGCGCGCAACATCGAGGAGGAGGAGGAGGCGCACGGGATAAGTT

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 82.40% 15.70% 1.95% 0.00% NA
All Indica  2759 99.30% 0.40% 0.33% 0.00% NA
All Japonica  1512 47.80% 47.30% 4.89% 0.00% NA
Aus  269 99.30% 0.00% 0.74% 0.00% NA
Indica I  595 99.50% 0.30% 0.17% 0.00% NA
Indica II  465 97.80% 1.30% 0.86% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.10% 0.40% 0.51% 0.00% NA
Temperate Japonica  767 12.50% 81.70% 5.74% 0.00% NA
Tropical Japonica  504 88.50% 8.30% 3.17% 0.00% NA
Japonica Intermediate  241 75.10% 19.10% 5.81% 0.00% NA
VI/Aromatic  96 93.80% 2.10% 4.17% 0.00% NA
Intermediate  90 81.10% 15.60% 3.33% 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
vg0318167000 A -> G LOC_Os03g31760.1 3_prime_UTR_variant ; 258.0bp to feature; MODIFIER silent_mutation Average:76.525; most accessible tissue: Zhenshan97 panicle, score: 88.888 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0318167000 NA 1.55E-12 mr1031 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
vg0318167000 NA 6.59E-13 mr1056 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
vg0318167000 NA 7.01E-06 mr1521 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
vg0318167000 NA 3.75E-06 mr1577 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
vg0318167000 NA 5.40E-07 mr1587 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
vg0318167000 NA 1.37E-07 mr1723 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
vg0318167000 NA 2.51E-06 mr1844 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
vg0318167000 NA 1.39E-11 mr1902 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
vg0318167000 NA 2.41E-09 mr1486_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
vg0318167000 2.39E-06 1.22E-08 mr1577_2 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
vg0318167000 NA 7.08E-07 mr1629_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
vg0318167000 NA 4.73E-07 mr1792_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
vg0318167000 1.28E-06 NA mr1803_2 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