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Detailed information for vg1209159762:

Variant ID: vg1209159762 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 9159762
Reference Allele: GAlternative Allele: A,T
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: 126. )

Flanking Sequence (100 bp) in Reference Genome:


GGGCCTCCAAGGCCCGTAGGACTCCTATTCGGATCCCTATCCGAATTAAGCTCATATTGGATCTCTATCCAATCCCCTTATTCCGGCCCATTAAGCATGC[G/A,T]
ACCCTGTAGGTTCATATATACTCGGCTGTAACCCGAAAACTCCTTTTTGGTCCACGCGTCAACAGCAGCCCCTAGCATAACGTATTGACCCACCGGGCAT

Reverse complement sequence

ATGCCCGGTGGGTCAATACGTTATGCTAGGGGCTGCTGTTGACGCGTGGACCAAAAAGGAGTTTTCGGGTTACAGCCGAGTATATATGAACCTACAGGGT[C/T,A]
GCATGCTTAATGGGCCGGAATAAGGGGATTGGATAGAGATCCAATATGAGCTTAATTCGGATAGGGATCCGAATAGGAGTCCTACGGGCCTTGGAGGCCC

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 97.20% 2.60% 0.28% 0.00% NA
All Indica  2759 96.70% 2.80% 0.43% 0.00% NA
All Japonica  1512 97.20% 2.80% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 89.20% 10.50% 0.22% 0.00% NA
Indica III  913 98.70% 0.10% 1.20% 0.00% NA
Indica Intermediate  786 96.60% 3.40% 0.00% 0.00% NA
Temperate Japonica  767 94.90% 5.10% 0.00% 0.00% NA
Tropical Japonica  504 99.40% 0.60% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 97.80% 1.10% 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
vg1209159762 G -> A LOC_Os12g16070.1 upstream_gene_variant ; 2376.0bp to feature; MODIFIER silent_mutation Average:22.684; most accessible tissue: Callus, score: 33.969 N N N N
vg1209159762 G -> A LOC_Os12g16060.1 intron_variant ; MODIFIER silent_mutation Average:22.684; most accessible tissue: Callus, score: 33.969 N N N N
vg1209159762 G -> T LOC_Os12g16070.1 upstream_gene_variant ; 2376.0bp to feature; MODIFIER N Average:22.684; most accessible tissue: Callus, score: 33.969 N N N N
vg1209159762 G -> T LOC_Os12g16060.1 intron_variant ; MODIFIER N Average:22.684; most accessible tissue: Callus, score: 33.969 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1209159762 6.78E-06 NA mr1912 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