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Detailed information for vg1116237651:

Variant ID: vg1116237651 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 16237651
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.96, A: 0.04, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:


CTGAGCCGGCCAGTGACTTCCTTGCCTCGGAGTATTTCGCCTAAGGGGTACTGTGAAGGCACTATGACTTTATTGGCCTGGAAGTAGTGCTTAAGCTTGC[G/A]
CGAAGCCATCACTAGAGCGTAAGCGAGCTTTTCCATTTCAATGTACCTTGTCTTCGCTCCTTGCAGTGCTTCGGAGACAAAGTAGACCGGTTTCTATCCG

Reverse complement sequence

CGGATAGAAACCGGTCTACTTTGTCTCCGAAGCACTGCAAGGAGCGAAGACAAGGTACATTGAAATGGAAAAGCTCGCTTACGCTCTAGTGATGGCTTCG[C/T]
GCAAGCTTAAGCACTACTTCCAGGCCAATAAAGTCATAGTGCCTTCACAGTACCCCTTAGGCGAAATACTCCGAGGCAAGGAAGTCACTGGCCGGCTCAG

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 56.30% 43.20% 0.47% 0.00% NA
All Indica  2759 30.00% 69.80% 0.25% 0.00% NA
All Japonica  1512 98.10% 1.90% 0.00% 0.00% NA
Aus  269 76.20% 18.60% 5.20% 0.00% NA
Indica I  595 29.70% 70.30% 0.00% 0.00% NA
Indica II  465 3.70% 96.30% 0.00% 0.00% NA
Indica III  913 42.70% 56.70% 0.55% 0.00% NA
Indica Intermediate  786 30.90% 68.80% 0.25% 0.00% NA
Temperate Japonica  767 98.00% 2.00% 0.00% 0.00% NA
Tropical Japonica  504 97.80% 2.20% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 92.70% 7.30% 0.00% 0.00% NA
Intermediate  90 62.20% 36.70% 1.11% 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
vg1116237651 G -> A LOC_Os11g28240.1 missense_variant ; p.Arg420Cys; MODERATE nonsynonymous_codon ; R420C Average:23.178; most accessible tissue: Zhenshan97 flag leaf, score: 40.929 benign 0.934 DELETERIOUS 0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1116237651 NA 2.10E-06 mr1246 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
vg1116237651 NA 1.50E-06 mr1834_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