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Detailed information for vg0317879120:

Variant ID: vg0317879120 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 17879120
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CGCGTCCAGTCCGGAGTCGCCACGCGTCTCGCCGAGCGCTCCGCGCGTGCTCCAGCCTAGCGGGCCTACCTGCCAGCGAGCGAAGCCACCGCTCCCGCGC[G/A]
GCCGCGCGCGCTTGCCAAAACTGCGTGGGTCCCGCGCCATGCCGCGTCTCACACCTTTCCTGCCGATGCCGTGGTCCGTCGAACGGGAGGCCGCCACGTT

Reverse complement sequence

AACGTGGCGGCCTCCCGTTCGACGGACCACGGCATCGGCAGGAAAGGTGTGAGACGCGGCATGGCGCGGGACCCACGCAGTTTTGGCAAGCGCGCGCGGC[C/T]
GCGCGGGAGCGGTGGCTTCGCTCGCTGGCAGGTAGGCCCGCTAGGCTGGAGCACGCGCGGAGCGCTCGGCGAGACGCGTGGCGACTCCGGACTGGACGCG

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 66.40% 1.10% 2.03% 30.47% NA
All Indica  2759 50.10% 1.80% 2.83% 45.23% NA
All Japonica  1512 92.10% 0.00% 0.13% 7.74% NA
Aus  269 81.00% 0.00% 5.20% 13.75% NA
Indica I  595 39.70% 0.00% 3.70% 56.64% NA
Indica II  465 62.40% 7.10% 3.44% 27.10% NA
Indica III  913 39.80% 0.20% 1.86% 58.16% NA
Indica Intermediate  786 62.80% 1.90% 2.93% 32.32% NA
Temperate Japonica  767 99.90% 0.00% 0.00% 0.13% NA
Tropical Japonica  504 79.20% 0.00% 0.20% 20.63% NA
Japonica Intermediate  241 94.60% 0.00% 0.41% 4.98% NA
VI/Aromatic  96 82.30% 0.00% 1.04% 16.67% NA
Intermediate  90 74.40% 0.00% 1.11% 24.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0317879120 G -> A LOC_Os03g31390.1 downstream_gene_variant ; 3798.0bp to feature; MODIFIER silent_mutation Average:25.034; most accessible tissue: Callus, score: 99.334 N N N N
vg0317879120 G -> A LOC_Os03g31370-LOC_Os03g31390 intergenic_region ; MODIFIER silent_mutation Average:25.034; most accessible tissue: Callus, score: 99.334 N N N N
vg0317879120 G -> DEL N N silent_mutation Average:25.034; most accessible tissue: Callus, score: 99.334 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0317879120 NA 2.75E-06 mr1310 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
vg0317879120 2.57E-15 3.46E-35 mr1498 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
vg0317879120 1.25E-10 8.42E-26 mr1769 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
vg0317879120 4.71E-06 4.71E-06 mr1916 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
vg0317879120 6.86E-08 1.79E-14 mr1925 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
vg0317879120 1.59E-12 4.57E-22 mr1951 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
vg0317879120 8.28E-06 2.95E-11 mr1310_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
vg0317879120 2.50E-11 2.80E-26 mr1498_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
vg0317879120 3.04E-12 4.04E-31 mr1769_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
vg0317879120 6.51E-07 4.46E-09 mr1916_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
vg0317879120 3.46E-07 9.01E-13 mr1925_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
vg0317879120 2.99E-08 1.44E-16 mr1951_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