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Detailed information for vg0915896376:

Variant ID: vg0915896376 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 15896376
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, T: 0.01, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:


ATGCTTGAGAATGCAACGGACATTGCTCCAGTCAAGGTTAAGTACATCTTGCACTATTGTTATGCACTTTTCTTTTGAGTGAGACCACCAAAAACAACAT[A/T]
GGAAATCCCCAAAATTGATATGGCAAAGCTATCTGAAATATACAGCCTTGACAAATTACGTTTTGCAAGAGGAGTACAAGCAAATTACAGAGCTAATAAC

Reverse complement sequence

GTTATTAGCTCTGTAATTTGCTTGTACTCCTCTTGCAAAACGTAATTTGTCAAGGCTGTATATTTCAGATAGCTTTGCCATATCAATTTTGGGGATTTCC[T/A]
ATGTTGTTTTTGGTGGTCTCACTCAAAAGAAAAGTGCATAACAATAGTGCAAGATGTACTTAACCTTGACTGGAGCAATGTCCGTTGCATTCTCAAGCAT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 55.30% 44.60% 0.11% 0.00% NA
All Indica  2759 26.90% 72.90% 0.18% 0.00% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 73.60% 26.40% 0.00% 0.00% NA
Indica I  595 10.60% 89.10% 0.34% 0.00% NA
Indica II  465 57.00% 43.00% 0.00% 0.00% NA
Indica III  913 18.00% 82.00% 0.00% 0.00% NA
Indica Intermediate  786 31.90% 67.70% 0.38% 0.00% NA
Temperate Japonica  767 99.60% 0.40% 0.00% 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 76.70% 23.30% 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
vg0915896376 A -> T LOC_Os09g26310.1 splice_region_variant ; LOW silent_mutation Average:65.741; most accessible tissue: Zhenshan97 flower, score: 88.827 N N N N
vg0915896376 A -> T LOC_Os09g26310.1 3_prime_UTR_variant ; 593.0bp to feature; MODIFIER silent_mutation Average:65.741; most accessible tissue: Zhenshan97 flower, score: 88.827 N N N N
vg0915896376 A -> T LOC_Os09g26300.1 upstream_gene_variant ; 3389.0bp to feature; MODIFIER silent_mutation Average:65.741; most accessible tissue: Zhenshan97 flower, score: 88.827 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0915896376 NA 2.80E-07 mr1739 Ind_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
vg0915896376 NA 2.53E-12 mr1904_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