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Detailed information for vg0127297735:

Variant ID: vg0127297735 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 27297735
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 281. )

Flanking Sequence (100 bp) in Reference Genome:


AAGGAACAAACAGGATCGTGATTCATGAGTAGCCGCGTGCGCCTACAAGAGACCCTTTCAGATAAACGAGCCAATAGCCGGATTTTATAAATTAACATAC[G/A]
AGAAAACGGCCCTTTCAAACACAATAGTTAATCAATTTGAATCACATATAGAATTTGTTCAATATACCATTTGAATAAAAGATTGCGCGTCTATGGAATA

Reverse complement sequence

TATTCCATAGACGCGCAATCTTTTATTCAAATGGTATATTGAACAAATTCTATATGTGATTCAAATTGATTAACTATTGTGTTTGAAAGGGCCGTTTTCT[C/T]
GTATGTTAATTTATAAAATCCGGCTATTGGCTCGTTTATCTGAAAGGGTCTCTTGTAGGCGCACGCGGCTACTCATGAATCACGATCCTGTTTGTTCCTT

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 96.50% 3.30% 0.13% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 89.30% 10.30% 0.40% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 79.10% 20.10% 0.78% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 98.90% 1.10% 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
vg0127297735 G -> A LOC_Os01g47730.1 upstream_gene_variant ; 3692.0bp to feature; MODIFIER silent_mutation Average:47.476; most accessible tissue: Callus, score: 81.776 N N N N
vg0127297735 G -> A LOC_Os01g47720.1 downstream_gene_variant ; 2287.0bp to feature; MODIFIER silent_mutation Average:47.476; most accessible tissue: Callus, score: 81.776 N N N N
vg0127297735 G -> A LOC_Os01g47710-LOC_Os01g47720 intergenic_region ; MODIFIER silent_mutation Average:47.476; most accessible tissue: Callus, score: 81.776 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0127297735 2.91E-06 NA mr1920 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