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Detailed information for vg0223694286:

Variant ID: vg0223694286 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 23694286
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 277. )

Flanking Sequence (100 bp) in Reference Genome:


CCGTTGGCTAAATCAGATGAAGTAGCTTTCTTACGGTCACATCGCACAATTAGCAATGCTCAAAAGGCTAATATTTTGGAATTGAAAGAAGTGGGTTTGC[G/A]
TCAGCATCAAGTTATGGATGTCATGGAGAGGCATCATGGTGGTTTTGATGCTACAGGTTTTGTTAGTAGGGACCTGTACAACTATTTTACTAGGCTAAGG

Reverse complement sequence

CCTTAGCCTAGTAAAATAGTTGTACAGGTCCCTACTAACAAAACCTGTAGCATCAAAACCACCATGATGCCTCTCCATGACATCCATAACTTGATGCTGA[C/T]
GCAAACCCACTTCTTTCAATTCCAAAATATTAGCCTTTTGAGCATTGCTAATTGTGCGATGTGACCGTAAGAAAGCTACTTCATCTGATTTAGCCAACGG

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 96.90% 0.10% 2.16% 0.87% NA
All Indica  2759 95.30% 0.00% 3.33% 1.34% NA
All Japonica  1512 99.70% 0.00% 0.33% 0.00% NA
Aus  269 97.40% 0.40% 0.74% 1.49% NA
Indica I  595 88.90% 0.00% 8.91% 2.18% NA
Indica II  465 97.80% 0.00% 0.86% 1.29% NA
Indica III  913 98.70% 0.10% 1.10% 0.11% NA
Indica Intermediate  786 94.70% 0.00% 3.18% 2.16% NA
Temperate Japonica  767 99.50% 0.00% 0.52% 0.00% NA
Tropical Japonica  504 99.80% 0.00% 0.20% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 1.00% 1.04% 0.00% NA
Intermediate  90 97.80% 0.00% 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
vg0223694286 G -> A LOC_Os02g39220.1 missense_variant ; p.Arg847His; MODERATE nonsynonymous_codon ; R847H Average:19.473; most accessible tissue: Zhenshan97 panicle, score: 32.308 benign 0.458 TOLERATED 0.16
vg0223694286 G -> DEL LOC_Os02g39220.1 N frameshift_variant Average:19.473; most accessible tissue: Zhenshan97 panicle, score: 32.308 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0223694286 3.99E-07 1.95E-07 mr1172_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