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Detailed information for vg0334056878:

Variant ID: vg0334056878 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 34056878
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.66, A: 0.34, others allele: 0.00, population size: 35. )

Flanking Sequence (100 bp) in Reference Genome:


CTCGTAAACATTTCTTTAGCTGAGACACATGGAAGACTGGGTGCACATCTGCGATATTCTCTGGTAACTGTAACTGATAGGCAACTTCTCCTCGTCTTGC[A/G]
ACGATTTGAAAAGGTCCCACATATCTTGGTGCTAGTTTTCCTTTGACCTTAAACCTTTTTGTTCCCCTCATCGGAGAAACCTTTAAATAGACGTAACTTC

Reverse complement sequence

GAAGTTACGTCTATTTAAAGGTTTCTCCGATGAGGGGAACAAAAAGGTTTAAGGTCAAAGGAAAACTAGCACCAAGATATGTGGGACCTTTTCAAATCGT[T/C]
GCAAGACGAGGAGAAGTTGCCTATCAGTTACAGTTACCAGAGAATATCGCAGATGTGCACCCAGTCTTCCATGTGTCTCAGCTAAAGAAATGTTTACGAG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 79.80% 0.40% 13.88% 5.86% NA
All Indica  2759 73.00% 0.50% 18.70% 7.76% NA
All Japonica  1512 99.70% 0.00% 0.07% 0.20% NA
Aus  269 40.50% 0.00% 48.33% 11.15% NA
Indica I  595 79.20% 1.00% 10.92% 8.91% NA
Indica II  465 63.70% 0.20% 23.23% 12.90% NA
Indica III  913 73.30% 0.00% 23.00% 3.72% NA
Indica Intermediate  786 73.50% 1.00% 16.92% 8.52% NA
Temperate Japonica  767 99.90% 0.00% 0.00% 0.13% NA
Tropical Japonica  504 99.60% 0.00% 0.20% 0.20% NA
Japonica Intermediate  241 99.60% 0.00% 0.00% 0.41% NA
VI/Aromatic  96 80.20% 0.00% 0.00% 19.79% NA
Intermediate  90 72.20% 5.60% 10.00% 12.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0334056878 A -> DEL LOC_Os03g59810.1 N frameshift_variant Average:14.849; most accessible tissue: Zhenshan97 young leaf, score: 23.991 N N N N
vg0334056878 A -> G LOC_Os03g59810.1 synonymous_variant ; p.Val1206Val; LOW synonymous_codon Average:14.849; most accessible tissue: Zhenshan97 young leaf, score: 23.991 N N N N
vg0334056878 A -> G LOC_Os03g59810.1 synonymous_variant ; p.Val1206Val; LOW nonsynonymous_codon ; V1206I Average:14.849; most accessible tissue: Zhenshan97 young leaf, score: 23.991 benign -0.069 TOLERATED 0.91

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0334056878 3.30E-06 1.05E-06 mr1679 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
vg0334056878 NA 1.70E-06 mr1693 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