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Detailed information for vg0819478073:

Variant ID: vg0819478073 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 19478073
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTCATATTTAAGTTTTTTCAAATAAGTTGTTCCTGTGCATGTACTCTCCGTCCTCTAATATAAGGGATTTTGATATTTTTCTTGTACTGTTTTACCATTC[A/G]
TCTTATTAAAAAAATTTGAAATTATTATTTATTTTATTTGTGACCTACTTTATTATCCAAAGTACTTTAAGCACAACTTTTCGGTTTAATATTTGCACAA

Reverse complement sequence

TTGTGCAAATATTAAACCGAAAAGTTGTGCTTAAAGTACTTTGGATAATAAAGTAGGTCACAAATAAAATAAATAATAATTTCAAATTTTTTTAATAAGA[T/C]
GAATGGTAAAACAGTACAAGAAAAATATCAAAATCCCTTATATTAGAGGACGGAGAGTACATGCACAGGAACAACTTATTTGAAAAAACTTAAATATGAA

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 63.90% 36.10% 0.04% 0.00% NA
All Indica  2759 94.60% 5.40% 0.00% 0.00% NA
All Japonica  1512 18.10% 81.80% 0.13% 0.00% NA
Aus  269 27.90% 72.10% 0.00% 0.00% NA
Indica I  595 99.00% 1.00% 0.00% 0.00% NA
Indica II  465 97.20% 2.80% 0.00% 0.00% NA
Indica III  913 94.00% 6.00% 0.00% 0.00% NA
Indica Intermediate  786 90.60% 9.40% 0.00% 0.00% NA
Temperate Japonica  767 0.70% 99.30% 0.00% 0.00% NA
Tropical Japonica  504 46.80% 52.80% 0.40% 0.00% NA
Japonica Intermediate  241 13.30% 86.70% 0.00% 0.00% NA
VI/Aromatic  96 10.40% 89.60% 0.00% 0.00% NA
Intermediate  90 56.70% 43.30% 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
vg0819478073 A -> G LOC_Os08g31480.1 upstream_gene_variant ; 4011.0bp to feature; MODIFIER silent_mutation Average:51.012; most accessible tissue: Minghui63 flag leaf, score: 79.085 N N N N
vg0819478073 A -> G LOC_Os08g31480-LOC_Os08g31510 intergenic_region ; MODIFIER silent_mutation Average:51.012; most accessible tissue: Minghui63 flag leaf, score: 79.085 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0819478073 7.97E-06 3.92E-08 mr1073 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
vg0819478073 NA 7.97E-14 mr1218 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
vg0819478073 NA 1.68E-06 mr1350 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
vg0819478073 NA 6.04E-19 mr1422 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
vg0819478073 NA 8.89E-06 mr1450 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
vg0819478073 NA 7.56E-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
vg0819478073 NA 9.83E-16 mr1583 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
vg0819478073 NA 1.00E-06 mr1830 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
vg0819478073 NA 3.47E-07 mr1850 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
vg0819478073 6.76E-08 NA mr1852 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
vg0819478073 4.95E-06 3.00E-10 mr1852 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
vg0819478073 NA 4.82E-06 mr1881 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