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Detailed information for vg0804574681:

Variant ID: vg0804574681 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 4574681
Reference Allele: AAlternative Allele: T
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.87, A: 0.13, others allele: 0.00, population size: 93. )

Flanking Sequence (100 bp) in Reference Genome:


GTAGGCTGATACTGCATTCAATACAAAAGAGTACTATATAGCAGCTTCCTTCTATGCAAAGGTTAAACCCACACTGTTTAATTCTGTTCCTTATTTTTTT[A/T]
AAAAAAAAGATTTTGTTGTCCTGTTCACGTTGATACTAAAAAATATATTCTCTTGGTTTCAGATGAATTATATCCTATCATTTGAGGAGATCAGCTTAAA

Reverse complement sequence

TTTAAGCTGATCTCCTCAAATGATAGGATATAATTCATCTGAAACCAAGAGAATATATTTTTTAGTATCAACGTGAACAGGACAACAAAATCTTTTTTTT[T/A]
AAAAAAATAAGGAACAGAATTAAACAGTGTGGGTTTAACCTTTGCATAGAAGGAAGCTGCTATATAGTACTCTTTTGTATTGAATGCAGTATCAGCCTAC

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 75.90% 23.00% 1.16% 0.00% NA
All Indica  2759 92.20% 7.70% 0.07% 0.00% NA
All Japonica  1512 48.60% 48.30% 3.11% 0.00% NA
Aus  269 64.70% 34.60% 0.74% 0.00% NA
Indica I  595 94.50% 5.50% 0.00% 0.00% NA
Indica II  465 92.90% 6.70% 0.43% 0.00% NA
Indica III  913 95.20% 4.80% 0.00% 0.00% NA
Indica Intermediate  786 86.80% 13.20% 0.00% 0.00% NA
Temperate Japonica  767 19.00% 77.20% 3.78% 0.00% NA
Tropical Japonica  504 85.90% 11.10% 2.98% 0.00% NA
Japonica Intermediate  241 64.70% 34.00% 1.24% 0.00% NA
VI/Aromatic  96 57.30% 38.50% 4.17% 0.00% NA
Intermediate  90 84.40% 15.60% 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
vg0804574681 A -> T LOC_Os08g08050.1 upstream_gene_variant ; 4748.0bp to feature; MODIFIER silent_mutation Average:41.416; most accessible tissue: Callus, score: 74.971 N N N N
vg0804574681 A -> T LOC_Os08g08060.1 intron_variant ; MODIFIER silent_mutation Average:41.416; most accessible tissue: Callus, score: 74.971 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0804574681 2.29E-06 2.29E-06 mr1542_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