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Detailed information for vg1100523028:

Variant ID: vg1100523028 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 523028
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, T: 0.01, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:


ATAAAGCTAGACTTGTTGCTCAAGGTTTTACCCAGGTGGAGAGTTTGGATTTTGATGAAACTTTTGCTTCTGTTGCTAGAATTGAGGCAATTAGACTTTT[G/T]
TTGGCTTTTGCTACTTCAAAAGGTTTTAAATTGTATCAAATGGATGTGAAAAGTGCTTTTCTAAATGGTTTTATACAGGAGGAAGTTTATGTCAAACAAC

Reverse complement sequence

GTTGTTTGACATAAACTTCCTCCTGTATAAAACCATTTAGAAAAGCACTTTTCACATCCATTTGATACAATTTAAAACCTTTTGAAGTAGCAAAAGCCAA[C/A]
AAAAGTCTAATTGCCTCAATTCTAGCAACAGAAGCAAAAGTTTCATCAAAATCCAAACTCTCCACCTGGGTAAAACCTTGAGCAACAAGTCTAGCTTTAT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 82.50% 17.50% 0.00% 0.00% NA
All Indica  2759 70.80% 29.20% 0.00% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 95.90% 4.10% 0.00% 0.00% NA
Indica I  595 70.90% 29.10% 0.00% 0.00% NA
Indica II  465 91.40% 8.60% 0.00% 0.00% NA
Indica III  913 56.20% 43.80% 0.00% 0.00% NA
Indica Intermediate  786 75.30% 24.70% 0.00% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 92.20% 7.80% 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
vg1100523028 G -> T LOC_Os11g01970.1 missense_variant ; p.Leu945Phe; MODERATE nonsynonymous_codon ; L945F Average:21.593; most accessible tissue: Callus, score: 31.08 benign 1.268 DELETERIOUS 0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1100523028 4.53E-06 5.12E-07 mr1863 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
vg1100523028 4.08E-07 4.08E-07 mr1863 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