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Detailed information for vg0202764681:

Variant ID: vg0202764681 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 2764681
Reference Allele: AAlternative Allele: T
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.83, A: 0.17, others allele: 0.00, population size: 104. )

Flanking Sequence (100 bp) in Reference Genome:


GTGTTTTTTGTAAAAATTTTCTATAGGAAATTTGCTTTAAAAAAATCATATTAATCCATTTTTTAAATTTAAAATAGTTAATACTCAATTAATCATGAGC[A/T]
AATAGCTCACCTCGTTTTGCGTATCCTCCTAATCTCCTCAATCCCCTTCTCCTCAAATACACCCTTAGTACTCGTTCTTGGCCATTTCATGTTGCACACA

Reverse complement sequence

TGTGTGCAACATGAAATGGCCAAGAACGAGTACTAAGGGTGTATTTGAGGAGAAGGGGATTGAGGAGATTAGGAGGATACGCAAAACGAGGTGAGCTATT[T/A]
GCTCATGATTAATTGAGTATTAACTATTTTAAATTTAAAAAATGGATTAATATGATTTTTTTAAAGCAAATTTCCTATAGAAAATTTTTACAAAAAACAC

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 54.30% 43.60% 1.71% 0.32% NA
All Indica  2759 79.40% 19.50% 1.09% 0.00% NA
All Japonica  1512 1.60% 94.20% 3.17% 0.99% NA
Aus  269 81.80% 18.20% 0.00% 0.00% NA
Indica I  595 60.20% 38.80% 1.01% 0.00% NA
Indica II  465 94.00% 4.30% 1.72% 0.00% NA
Indica III  913 78.20% 21.10% 0.66% 0.00% NA
Indica Intermediate  786 86.80% 12.00% 1.27% 0.00% NA
Temperate Japonica  767 0.70% 97.00% 2.35% 0.00% NA
Tropical Japonica  504 2.00% 95.40% 1.39% 1.19% NA
Japonica Intermediate  241 3.70% 83.00% 9.54% 3.73% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 42.20% 54.40% 3.33% 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
vg0202764681 A -> T LOC_Os02g05650.1 upstream_gene_variant ; 1799.0bp to feature; MODIFIER silent_mutation Average:65.027; most accessible tissue: Minghui63 flower, score: 82.891 N N N N
vg0202764681 A -> T LOC_Os02g05660.1 downstream_gene_variant ; 1536.0bp to feature; MODIFIER silent_mutation Average:65.027; most accessible tissue: Minghui63 flower, score: 82.891 N N N N
vg0202764681 A -> T LOC_Os02g05650-LOC_Os02g05660 intergenic_region ; MODIFIER silent_mutation Average:65.027; most accessible tissue: Minghui63 flower, score: 82.891 N N N N
vg0202764681 A -> DEL N N silent_mutation Average:65.027; most accessible tissue: Minghui63 flower, score: 82.891 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0202764681 8.66E-06 8.66E-06 mr1598 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
vg0202764681 4.69E-06 8.81E-06 mr1613 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
vg0202764681 NA 2.66E-09 mr1761 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
vg0202764681 1.02E-06 1.02E-06 mr1795 Jap_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
vg0202764681 NA 2.33E-06 mr1913 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
vg0202764681 NA 4.76E-18 mr1557_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