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Detailed information for vg0317018800:

Variant ID: vg0317018800 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 17018800
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 313. )

Flanking Sequence (100 bp) in Reference Genome:


ACCACTTGCACTAACCTGCGAGATCCCGAAAGGCGAACCCAAAATCCCGGCCTGATCAGAGCAGCTGGCCACCCGCTTCATCGAACGGGCCAACTCAGCA[C/A]
ACTCTTGCTGCACCTTGCCGACGGAATCCATGGCGAGATCCACCTTGGTAGTCACCTTCTCGAGACTGCCACTTTGGGAATCCAGCCGCTGATCAATCTC

Reverse complement sequence

GAGATTGATCAGCGGCTGGATTCCCAAAGTGGCAGTCTCGAGAAGGTGACTACCAAGGTGGATCTCGCCATGGATTCCGTCGGCAAGGTGCAGCAAGAGT[G/T]
TGCTGAGTTGGCCCGTTCGATGAAGCGGGTGGCCAGCTGCTCTGATCAGGCCGGGATTTTGGGTTCGCCTTTCGGGATCTCGCAGGTTAGTGCAAGTGGT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 96.40% 3.40% 0.19% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 88.70% 10.70% 0.60% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 78.50% 20.30% 1.17% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 97.50% 2.50% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 98.90% 1.10% 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
vg0317018800 C -> A LOC_Os03g29864.1 missense_variant ; p.Cys505Phe; MODERATE nonsynonymous_codon ; C505F Average:34.413; most accessible tissue: Minghui63 flag leaf, score: 72.028 unknown unknown DELETERIOUS 0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0317018800 NA 2.38E-06 mr1210 Jap_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
vg0317018800 1.81E-06 7.03E-08 mr1897 Jap_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
vg0317018800 NA 6.12E-06 mr1305_2 Jap_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
vg0317018800 NA 4.36E-07 mr1733_2 Jap_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