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Detailed information for vg0905652760:

Variant ID: vg0905652760 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 5652760
Reference Allele: AAlternative Allele: T
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.84, T: 0.18, others allele: 0.00, population size: 55. )

Flanking Sequence (100 bp) in Reference Genome:


TCCTCCATTACTAAAGGAAAAGCATAGGGAAATATAATCCACTCCAACCTAATGTTTGCATTCCTTTGGTTGGCTTGCTCAACAACATAGGAAAAATTCC[A/T]
ATGTTTTTCAATCTATAGGTTTGCACATGTATTCCTGTAGTATTCATATGTTTTTCCTATTTCTACGTTTTGAAAATCCTGTGAACCGAACGAGCCCTTA

Reverse complement sequence

TAAGGGCTCGTTCGGTTCACAGGATTTTCAAAACGTAGAAATAGGAAAAACATATGAATACTACAGGAATACATGTGCAAACCTATAGATTGAAAAACAT[T/A]
GGAATTTTTCCTATGTTGTTGAGCAAGCCAACCAAAGGAATGCAAACATTAGGTTGGAGTGGATTATATTTCCCTATGCTTTTCCTTTAGTAATGGAGGA

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 71.60% 28.40% 0.02% 0.00% NA
All Indica  2759 97.20% 2.80% 0.00% 0.00% NA
All Japonica  1512 20.30% 79.60% 0.07% 0.00% NA
Aus  269 91.80% 8.20% 0.00% 0.00% NA
Indica I  595 99.00% 1.00% 0.00% 0.00% NA
Indica II  465 92.00% 8.00% 0.00% 0.00% NA
Indica III  913 98.10% 1.90% 0.00% 0.00% NA
Indica Intermediate  786 97.70% 2.30% 0.00% 0.00% NA
Temperate Japonica  767 10.70% 89.20% 0.13% 0.00% NA
Tropical Japonica  504 18.50% 81.50% 0.00% 0.00% NA
Japonica Intermediate  241 54.80% 45.20% 0.00% 0.00% NA
VI/Aromatic  96 96.90% 3.10% 0.00% 0.00% NA
Intermediate  90 60.00% 40.00% 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
vg0905652760 A -> T LOC_Os09g10350.1 upstream_gene_variant ; 2792.0bp to feature; MODIFIER silent_mutation Average:25.356; most accessible tissue: Callus, score: 52.452 N N N N
vg0905652760 A -> T LOC_Os09g10340-LOC_Os09g10350 intergenic_region ; MODIFIER silent_mutation Average:25.356; most accessible tissue: Callus, score: 52.452 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0905652760 7.52E-07 1.82E-06 mr1697 Ind_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
vg0905652760 NA 4.18E-08 mr1299_2 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
vg0905652760 NA 1.61E-08 mr1700_2 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