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Detailed information for vg0802505868:

Variant ID: vg0802505868 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 2505868
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 295. )

Flanking Sequence (100 bp) in Reference Genome:


TGACGGATTTAACTCTTTGATGTTCCCTGTCATGTTGGTTGCAGGATCAAACCATCTGGCACGCTCAGAACCCGAAGGCAAATTTCCTGGACCTGCACTG[G/A]
AGTTAAGCATATCTCCTAGGCCCCTACGTGTCGATTTTTCGAGTCAACAGCCGCCCCCGGAGCCGTAAGCGCGCTCCAGAGGCTACGATTGCCTCCGCGA

Reverse complement sequence

TCGCGGAGGCAATCGTAGCCTCTGGAGCGCGCTTACGGCTCCGGGGGCGGCTGTTGACTCGAAAAATCGACACGTAGGGGCCTAGGAGATATGCTTAACT[C/T]
CAGTGCAGGTCCAGGAAATTTGCCTTCGGGTTCTGAGCGTGCCAGATGGTTTGATCCTGCAACCAACATGACAGGGAACATCAAAGAGTTAAATCCGTCA

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 94.60% 4.60% 0.74% 0.00% NA
All Indica  2759 91.00% 7.80% 1.20% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 93.80% 4.00% 2.18% 0.00% NA
Indica II  465 95.10% 4.90% 0.00% 0.00% NA
Indica III  913 87.20% 12.00% 0.77% 0.00% NA
Indica Intermediate  786 90.80% 7.50% 1.65% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 0.00% 1.04% 0.00% NA
Intermediate  90 96.70% 2.20% 1.11% 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
vg0802505868 G -> A LOC_Os08g04920.3 downstream_gene_variant ; 1502.0bp to feature; MODIFIER silent_mutation Average:67.355; most accessible tissue: Minghui63 panicle, score: 87.238 N N N N
vg0802505868 G -> A LOC_Os08g04920.1 downstream_gene_variant ; 1394.0bp to feature; MODIFIER silent_mutation Average:67.355; most accessible tissue: Minghui63 panicle, score: 87.238 N N N N
vg0802505868 G -> A LOC_Os08g04920.5 downstream_gene_variant ; 1394.0bp to feature; MODIFIER silent_mutation Average:67.355; most accessible tissue: Minghui63 panicle, score: 87.238 N N N N
vg0802505868 G -> A LOC_Os08g04920.4 downstream_gene_variant ; 1454.0bp to feature; MODIFIER silent_mutation Average:67.355; most accessible tissue: Minghui63 panicle, score: 87.238 N N N N
vg0802505868 G -> A LOC_Os08g04920.6 downstream_gene_variant ; 1454.0bp to feature; MODIFIER silent_mutation Average:67.355; most accessible tissue: Minghui63 panicle, score: 87.238 N N N N
vg0802505868 G -> A LOC_Os08g04920.8 downstream_gene_variant ; 1457.0bp to feature; MODIFIER silent_mutation Average:67.355; most accessible tissue: Minghui63 panicle, score: 87.238 N N N N
vg0802505868 G -> A LOC_Os08g04920.7 downstream_gene_variant ; 2256.0bp to feature; MODIFIER silent_mutation Average:67.355; most accessible tissue: Minghui63 panicle, score: 87.238 N N N N
vg0802505868 G -> A LOC_Os08g04920.2 downstream_gene_variant ; 2277.0bp to feature; MODIFIER silent_mutation Average:67.355; most accessible tissue: Minghui63 panicle, score: 87.238 N N N N
vg0802505868 G -> A LOC_Os08g04910-LOC_Os08g04920 intergenic_region ; MODIFIER silent_mutation Average:67.355; most accessible tissue: Minghui63 panicle, score: 87.238 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0802505868 1.56E-06 2.05E-08 mr1425_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