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Detailed information for vg0314891809:

Variant ID: vg0314891809 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 14891809
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CGCCACATGGCAGTTGGGCGAGGGCCTCGGGGCGAGGCAGCGCGAGGGCCCGAGGGGTGTGACGTGGAACCCCGAGGCCCCCTGGCTGCTTCTGCGACTC[G/A]
CGAGACGCGGGGGGAGGGCCAGGCTGTAGAGCCACGTGGCTGGATGGGAAGGTGACTTCCCCTCACTTTGCATTCCCCCGGGCCTATATCTCCGATAGCC

Reverse complement sequence

GGCTATCGGAGATATAGGCCCGGGGGAATGCAAAGTGAGGGGAAGTCACCTTCCCATCCAGCCACGTGGCTCTACAGCCTGGCCCTCCCCCCGCGTCTCG[C/T]
GAGTCGCAGAAGCAGCCAGGGGGCCTCGGGGTTCCACGTCACACCCCTCGGGCCCTCGCGCTGCCTCGCCCCGAGGCCCTCGCCCAACTGCCATGTGGCG

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 89.40% 9.90% 0.66% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 67.50% 30.50% 2.05% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 39.10% 56.80% 4.04% 0.00% NA
Tropical Japonica  504 98.80% 1.20% 0.00% 0.00% NA
Japonica Intermediate  241 92.10% 7.90% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 93.30% 6.70% 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
vg0314891809 G -> A LOC_Os03g25990.1 upstream_gene_variant ; 2905.0bp to feature; MODIFIER silent_mutation Average:72.781; most accessible tissue: Zhenshan97 panicle, score: 87.764 N N N N
vg0314891809 G -> A LOC_Os03g25984.1 downstream_gene_variant ; 2164.0bp to feature; MODIFIER silent_mutation Average:72.781; most accessible tissue: Zhenshan97 panicle, score: 87.764 N N N N
vg0314891809 G -> A LOC_Os03g25984-LOC_Os03g25990 intergenic_region ; MODIFIER silent_mutation Average:72.781; most accessible tissue: Zhenshan97 panicle, score: 87.764 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0314891809 2.36E-06 5.83E-23 mr1115 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
vg0314891809 NA 1.38E-06 mr1252 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
vg0314891809 4.06E-06 NA mr1305 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
vg0314891809 NA 3.74E-06 mr1482 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
vg0314891809 NA 2.22E-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
vg0314891809 NA 2.22E-07 mr1576 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
vg0314891809 3.63E-08 6.16E-24 mr1611 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
vg0314891809 6.90E-07 NA mr1611 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
vg0314891809 NA 1.14E-09 mr1712 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
vg0314891809 NA 1.94E-08 mr1763 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
vg0314891809 NA 4.69E-07 mr1837 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
vg0314891809 NA 2.36E-06 mr1880 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
vg0314891809 NA 3.58E-08 mr1977 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