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Detailed information for vg0335767848:

Variant ID: vg0335767848 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 35767848
Reference Allele: CAlternative Allele: A
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.58, C: 0.42, others allele: 0.00, population size: 89. )

Flanking Sequence (100 bp) in Reference Genome:


TGTACTTGTTTCGAGTGTACGAAAAGTGGCAAAGAAAGTCCTAGGATCTTACACCACCTAGTGATTCACGCTAATTTGATCATCAATGGCGGCAGGGCGG[C/A]
GAGTTCCGGGGGTTGGCGGCGGCGGTGGCGCGGGCGGCGACGGATGACCGGACGGTGATCATCACGTGCGTGAACCACGCGTTCGCGGCGCCCGACTCGC

Reverse complement sequence

GCGAGTCGGGCGCCGCGAACGCGTGGTTCACGCACGTGATGATCACCGTCCGGTCATCCGTCGCCGCCCGCGCCACCGCCGCCGCCAACCCCCGGAACTC[G/T]
CCGCCCTGCCGCCATTGATGATCAAATTAGCGTGAATCACTAGGTGGTGTAAGATCCTAGGACTTTCTTTGCCACTTTTCGTACACTCGAAACAAGTACA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 54.70% 45.20% 0.13% 0.00% NA
All Indica  2759 80.80% 19.00% 0.18% 0.00% NA
All Japonica  1512 2.30% 97.70% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 97.30% 2.50% 0.17% 0.00% NA
Indica II  465 85.20% 14.80% 0.00% 0.00% NA
Indica III  913 67.10% 32.90% 0.00% 0.00% NA
Indica Intermediate  786 81.70% 17.80% 0.51% 0.00% NA
Temperate Japonica  767 0.80% 99.20% 0.00% 0.00% NA
Tropical Japonica  504 5.40% 94.60% 0.00% 0.00% NA
Japonica Intermediate  241 0.80% 99.20% 0.00% 0.00% NA
VI/Aromatic  96 3.10% 96.90% 0.00% 0.00% NA
Intermediate  90 54.40% 44.40% 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
vg0335767848 C -> A LOC_Os03g63280.1 synonymous_variant ; p.Gly127Gly; LOW synonymous_codon Average:67.737; most accessible tissue: Zhenshan97 panicle, score: 84.374 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0335767848 NA 5.75E-23 mr1383 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
vg0335767848 NA 1.67E-33 mr1723 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
vg0335767848 NA 1.21E-17 mr1767 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
vg0335767848 NA 1.27E-11 mr1846 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
vg0335767848 NA 4.45E-14 mr1924 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
vg0335767848 NA 5.13E-06 mr1120_2 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
vg0335767848 NA 1.55E-34 mr1723_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