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Detailed information for vg0317962584:

Variant ID: vg0317962584 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 17962584
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 359. )

Flanking Sequence (100 bp) in Reference Genome:


CCGTGTCCATCCTTGTTAGGATTAGCGGTGATGGTCTTGTAAAGGGCATCTTTTGAATGGTATGTCTTCATGCATCCATATTTCACCAATGTGCCCAACC[T/C]
CTCATTCTCTTTCTTAAGAGCTTGCATAGCATCAACATTAGTAGCATAAGAGTTCAAATCAATATTGTAACACCTAGCACAACCATTGCTAGTAGATGGA

Reverse complement sequence

TCCATCTACTAGCAATGGTTGTGCTAGGTGTTACAATATTGATTTGAACTCTTATGCTACTAATGTTGATGCTATGCAAGCTCTTAAGAAAGAGAATGAG[A/G]
GGTTGGGCACATTGGTGAAATATGGATGCATGAAGACATACCATTCAAAAGATGCCCTTTACAAGACCATCACCGCTAATCCTAACAAGGATGGACACGG

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 96.70% 2.60% 0.74% 0.00% NA
All Indica  2759 99.90% 0.00% 0.07% 0.00% NA
All Japonica  1512 90.90% 7.90% 1.19% 0.00% NA
Aus  269 96.30% 0.00% 3.72% 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 99.70% 0.00% 0.25% 0.00% NA
Temperate Japonica  767 97.50% 1.80% 0.65% 0.00% NA
Tropical Japonica  504 83.90% 14.50% 1.59% 0.00% NA
Japonica Intermediate  241 84.20% 13.70% 2.07% 0.00% NA
VI/Aromatic  96 96.90% 0.00% 3.12% 0.00% NA
Intermediate  90 96.70% 1.10% 2.22% 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
vg0317962584 T -> C LOC_Os03g31530.1 missense_variant ; p.Arg358Gly; MODERATE nonsynonymous_codon ; R358G Average:32.535; most accessible tissue: Minghui63 flag leaf, score: 61.847 benign 1.478 TOLERATED 0.11

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0317962584 NA 1.34E-07 mr1040 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
vg0317962584 1.37E-07 4.98E-10 mr1836_2 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