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Detailed information for vg0316491917:

Variant ID: vg0316491917 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 16491917
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.84, T: 0.15, G: 0.01, others allele: 0.00, population size: 101. )

Flanking Sequence (100 bp) in Reference Genome:


CTCGTTTTAGGGTTTCTGCCGGTATCGGCTAAATCGCGTTGCTAGATTAGATTAGCTTAGACATCTACTACCCTGAAAATTCAGTCGACGGCTTGATTGT[C/T]
TAGATATTGTGTTTCTTTTCATACTTAGTGCTGCATCAATTAAGTTTGATCTACTAAGTCGTGCTTAGAACCATAATCTCTAGCCTGCCTTTGACTGCCA

Reverse complement sequence

TGGCAGTCAAAGGCAGGCTAGAGATTATGGTTCTAAGCACGACTTAGTAGATCAAACTTAATTGATGCAGCACTAAGTATGAAAAGAAACACAATATCTA[G/A]
ACAATCAAGCCGTCGACTGAATTTTCAGGGTAGTAGATGTCTAAGCTAATCTAATCTAGCAACGCGATTTAGCCGATACCGGCAGAAACCCTAAAACGAG

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 49.90% 37.00% 0.63% 12.51% NA
All Indica  2759 75.60% 19.50% 0.80% 4.06% NA
All Japonica  1512 1.80% 70.90% 0.40% 26.92% NA
Aus  269 72.50% 5.90% 0.37% 21.19% NA
Indica I  595 60.00% 40.00% 0.00% 0.00% NA
Indica II  465 92.30% 5.80% 0.22% 1.72% NA
Indica III  913 78.10% 15.20% 1.53% 5.15% NA
Indica Intermediate  786 74.70% 17.20% 0.89% 7.25% NA
Temperate Japonica  767 1.70% 55.70% 0.52% 42.11% NA
Tropical Japonica  504 2.20% 89.10% 0.40% 8.33% NA
Japonica Intermediate  241 1.20% 81.30% 0.00% 17.43% NA
VI/Aromatic  96 8.30% 87.50% 0.00% 4.17% NA
Intermediate  90 44.40% 42.20% 1.11% 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
vg0316491917 C -> T LOC_Os03g29035.1 intron_variant ; MODIFIER silent_mutation Average:36.455; most accessible tissue: Zhenshan97 flag leaf, score: 56.722 N N N N
vg0316491917 C -> DEL N N silent_mutation Average:36.455; most accessible tissue: Zhenshan97 flag leaf, score: 56.722 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0316491917 NA 3.76E-07 mr1542 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
vg0316491917 NA 1.89E-07 mr1020_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
vg0316491917 NA 1.95E-14 mr1162_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
vg0316491917 1.85E-06 3.77E-06 mr1296_2 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
vg0316491917 NA 6.45E-06 mr1355_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
vg0316491917 NA 6.56E-06 mr1452_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
vg0316491917 NA 3.38E-09 mr1542_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
vg0316491917 5.19E-06 3.03E-13 mr1666_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
vg0316491917 NA 2.51E-11 mr1749_2 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
vg0316491917 6.95E-06 3.85E-13 mr1761_2 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
vg0316491917 NA 4.12E-06 mr1761_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
vg0316491917 NA 6.82E-08 mr1821_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