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Detailed information for vg0103794839:

Variant ID: vg0103794839 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 3794839
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.83, A: 0.18, others allele: 0.00, population size: 80. )

Flanking Sequence (100 bp) in Reference Genome:


TAGTGAATTTCGACATGTAGAACTCAAGAAAAATTCCACATGCCAATTCCGATTATTATTTGCATTGATTTAATAGGGTTTACTCTTGCTTTGCACCGGT[G/A]
TTTTCTTAGAGTCTCTTATTAATTCAATTTTAGGCTTAGGAGGAGAACTTCAGGGTGTGACAAATATGTACACCCGGGGCCATTGTAATATATCAATCTA

Reverse complement sequence

TAGATTGATATATTACAATGGCCCCGGGTGTACATATTTGTCACACCCTGAAGTTCTCCTCCTAAGCCTAAAATTGAATTAATAAGAGACTCTAAGAAAA[C/T]
ACCGGTGCAAAGCAAGAGTAAACCCTATTAAATCAATGCAAATAATAATCGGAATTGGCATGTGGAATTTTTCTTGAGTTCTACATGTCGAAATTCACTA

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 30.00% 0.90% 5.06% 64.03% NA
All Indica  2759 1.60% 1.50% 4.82% 92.03% NA
All Japonica  1512 84.30% 0.10% 5.95% 9.59% NA
Aus  269 2.60% 0.00% 3.72% 93.68% NA
Indica I  595 2.00% 1.30% 3.19% 93.45% NA
Indica II  465 1.30% 0.40% 3.44% 94.84% NA
Indica III  913 1.20% 2.80% 6.79% 89.16% NA
Indica Intermediate  786 2.00% 0.80% 4.58% 92.62% NA
Temperate Japonica  767 94.80% 0.00% 0.00% 5.22% NA
Tropical Japonica  504 67.50% 0.40% 17.06% 15.08% NA
Japonica Intermediate  241 86.30% 0.00% 1.66% 12.03% NA
VI/Aromatic  96 53.10% 0.00% 1.04% 45.83% NA
Intermediate  90 43.30% 0.00% 5.56% 51.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0103794839 G -> A LOC_Os01g07860-LOC_Os01g07870 intergenic_region ; MODIFIER silent_mutation Average:24.977; most accessible tissue: Zhenshan97 panicle, score: 46.362 N N N N
vg0103794839 G -> DEL N N silent_mutation Average:24.977; most accessible tissue: Zhenshan97 panicle, score: 46.362 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0103794839 NA 4.83E-06 mr1066 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
vg0103794839 NA 2.35E-17 mr1304 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
vg0103794839 NA 5.91E-27 mr1414 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
vg0103794839 NA 3.15E-24 mr1571 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
vg0103794839 NA 2.89E-07 mr1659 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
vg0103794839 NA 1.18E-10 mr1683 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
vg0103794839 NA 2.04E-20 mr1838 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
vg0103794839 NA 2.85E-10 mr1904 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
vg0103794839 NA 7.03E-06 mr1925 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