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Detailed information for vg0317274577:

Variant ID: vg0317274577 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 17274577
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.02, others allele: 0.00, population size: 209. )

Flanking Sequence (100 bp) in Reference Genome:


AATGATGCAGACGTGCAAGGGGAACACAAGGACGGTTTGTGGCTATTTGCATAAAGGCGGATGTAAAACATTTTATTAAGCAAAACAGTAAAACAGTTGA[G/A]
TGATTAAAGTAACATTAAATCTCCACTGATCAACGCTACACCACGTTGAACAGGCCCAACCAACCCACCTGAACTACTGTGCATTGAGTCGATTTATTAA

Reverse complement sequence

TTAATAAATCGACTCAATGCACAGTAGTTCAGGTGGGTTGGTTGGGCCTGTTCAACGTGGTGTAGCGTTGATCAGTGGAGATTTAATGTTACTTTAATCA[C/T]
TCAACTGTTTTACTGTTTTGCTTAATAAAATGTTTTACATCCGCCTTTATGCAAATAGCCACAAACCGTCCTTGTGTTCCCCTTGCACGTCTGCATCATT

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 93.50% 6.50% 0.02% 0.00% NA
All Indica  2759 97.00% 3.00% 0.00% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 21.20% 78.40% 0.37% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.40% 0.60% 0.00% 0.00% NA
Indica III  913 97.00% 3.00% 0.00% 0.00% NA
Indica Intermediate  786 93.10% 6.90% 0.00% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 92.70% 7.30% 0.00% 0.00% NA
Intermediate  90 96.70% 3.30% 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
vg0317274577 G -> A LOC_Os03g30264.1 upstream_gene_variant ; 2585.0bp to feature; MODIFIER silent_mutation Average:64.464; most accessible tissue: Minghui63 young leaf, score: 75.006 N N N N
vg0317274577 G -> A LOC_Os03g30270.1 upstream_gene_variant ; 1408.0bp to feature; MODIFIER silent_mutation Average:64.464; most accessible tissue: Minghui63 young leaf, score: 75.006 N N N N
vg0317274577 G -> A LOC_Os03g30280.1 downstream_gene_variant ; 4028.0bp to feature; MODIFIER silent_mutation Average:64.464; most accessible tissue: Minghui63 young leaf, score: 75.006 N N N N
vg0317274577 G -> A LOC_Os03g30264-LOC_Os03g30270 intergenic_region ; MODIFIER silent_mutation Average:64.464; most accessible tissue: Minghui63 young leaf, score: 75.006 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0317274577 NA 6.31E-06 mr1030 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
vg0317274577 NA 5.47E-07 mr1053 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
vg0317274577 NA 2.20E-09 mr1157 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
vg0317274577 NA 6.93E-06 mr1319 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
vg0317274577 NA 7.01E-08 mr1328 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
vg0317274577 NA 5.87E-07 mr1373 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
vg0317274577 NA 7.27E-09 mr1446 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
vg0317274577 NA 1.56E-12 mr1499 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
vg0317274577 NA 2.38E-06 mr1652 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
vg0317274577 NA 1.82E-07 mr1952 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
vg0317274577 NA 6.79E-09 mr1989 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
vg0317274577 9.17E-07 NA mr1270_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
vg0317274577 NA 1.93E-08 mr1612_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