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Detailed information for vg0602872794:

Variant ID: vg0602872794 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 2872794
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 318. )

Flanking Sequence (100 bp) in Reference Genome:


AGGCCATGTGCTATTTGCATGGGTGTTTTTTGCTCCAACTGCAGCTAATGGCATACGGAAATTCCGGTGCCCGTGAAGAACCAAATGAAAAAAGAGGTAG[C/A]
CATGACAAGTTGTTAGCATGCCGTTTTAAAGCTAGGGAATACCGCAAGGATCACGTAGAAGTGCTCACCGTGTCAATCGGATCTAAATTCAAATTTCTAC

Reverse complement sequence

GTAGAAATTTGAATTTAGATCCGATTGACACGGTGAGCACTTCTACGTGATCCTTGCGGTATTCCCTAGCTTTAAAACGGCATGCTAACAACTTGTCATG[G/T]
CTACCTCTTTTTTCATTTGGTTCTTCACGGGCACCGGAATTTCCGTATGCCATTAGCTGCAGTTGGAGCAAAAAACACCCATGCAAATAGCACATGGCCT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 98.10% 1.30% 0.59% 0.00% NA
All Indica  2759 99.80% 0.00% 0.18% 0.00% NA
All Japonica  1512 94.60% 3.90% 1.52% 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 99.40% 0.20% 0.43% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.60% 0.00% 0.38% 0.00% NA
Temperate Japonica  767 91.70% 6.10% 2.22% 0.00% NA
Tropical Japonica  504 99.20% 0.40% 0.40% 0.00% NA
Japonica Intermediate  241 94.20% 4.10% 1.66% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg0602872794 C -> A LOC_Os06g06200.1 upstream_gene_variant ; 94.0bp to feature; MODIFIER silent_mutation Average:42.046; most accessible tissue: Callus, score: 63.462 N N N N
vg0602872794 C -> A LOC_Os06g06210.2 upstream_gene_variant ; 1556.0bp to feature; MODIFIER silent_mutation Average:42.046; most accessible tissue: Callus, score: 63.462 N N N N
vg0602872794 C -> A LOC_Os06g06220.1 upstream_gene_variant ; 4646.0bp to feature; MODIFIER silent_mutation Average:42.046; most accessible tissue: Callus, score: 63.462 N N N N
vg0602872794 C -> A LOC_Os06g06200-LOC_Os06g06210 intergenic_region ; MODIFIER silent_mutation Average:42.046; most accessible tissue: Callus, score: 63.462 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0602872794 NA 1.64E-09 mr1757 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
vg0602872794 1.64E-07 1.22E-10 mr1549_2 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
vg0602872794 1.04E-06 3.02E-08 mr1550_2 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
vg0602872794 5.81E-07 1.38E-09 mr1757_2 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