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Detailed information for vg0808431807:

Variant ID: vg0808431807 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 8431807
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:


TATTAATCAACATAAAGAAGAAGCACATTAATTTGTGCATTTATAATTATACTACTACATCTATCAGTGGTGTATCTTAAAAATAAAAAGAGCCCAAGTA[A/G]
ACTTATTTGCTATAAAAACTCTGTTTCAATCTTCTAATATATAATTTCAATGGATTCAGCAATGAGCCTGGGCAGCCGCCTGAGGTTGCTAGGGACAAAA

Reverse complement sequence

TTTTGTCCCTAGCAACCTCAGGCGGCTGCCCAGGCTCATTGCTGAATCCATTGAAATTATATATTAGAAGATTGAAACAGAGTTTTTATAGCAAATAAGT[T/C]
TACTTGGGCTCTTTTTATTTTTAAGATACACCACTGATAGATGTAGTAGTATAATTATAAATGCACAAATTAATGTGCTTCTTCTTTATGTTGATTAATA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 90.30% 9.60% 0.06% 0.00% NA
All Indica  2759 88.50% 11.40% 0.11% 0.00% NA
All Japonica  1512 91.40% 8.60% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 92.80% 7.20% 0.00% 0.00% NA
Indica II  465 95.10% 4.90% 0.00% 0.00% NA
Indica III  913 78.30% 21.40% 0.33% 0.00% NA
Indica Intermediate  786 93.10% 6.90% 0.00% 0.00% NA
Temperate Japonica  767 99.10% 0.90% 0.00% 0.00% NA
Tropical Japonica  504 82.90% 17.10% 0.00% 0.00% NA
Japonica Intermediate  241 84.60% 15.40% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 88.90% 11.10% 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
vg0808431807 A -> G LOC_Os08g14090.1 intron_variant ; MODIFIER silent_mutation Average:57.348; most accessible tissue: Callus, score: 66.995 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0808431807 NA 6.49E-07 mr1397_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
vg0808431807 1.33E-06 NA mr1555_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
vg0808431807 NA 2.98E-06 mr1600_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
vg0808431807 NA 5.84E-06 mr1663_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
vg0808431807 3.73E-06 3.73E-06 mr1674_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
vg0808431807 6.20E-06 6.19E-06 mr1822_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
vg0808431807 NA 8.31E-06 mr1843_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
vg0808431807 NA 6.16E-06 mr1888_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
vg0808431807 4.01E-06 3.60E-06 mr1982_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