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Detailed information for vg0904455249:

Variant ID: vg0904455249 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 4455249
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 123. )

Flanking Sequence (100 bp) in Reference Genome:


GAGGAGCTCTGCCAAATTGCCTGTTCTCATAGTTCAACAAAATAGAGTACAATTCTGCGACGGTAACAGGTTCTACTCTTGTCACCAGTCTAGAGATAGC[A/T]
GGTTCATATTCATCATCTAATCCATTCAATATAAAAGCTACTAGATCTTCTTCATCCATGGTTTTACCACATGTGCGGCAGGGGCAGCAACAATCAGCAG

Reverse complement sequence

CTGCTGATTGTTGCTGCCCCTGCCGCACATGTGGTAAAACCATGGATGAAGAAGATCTAGTAGCTTTTATATTGAATGGATTAGATGATGAATATGAACC[T/A]
GCTATCTCTAGACTGGTGACAAGAGTAGAACCTGTTACCGTCGCAGAATTGTACTCTATTTTGTTGAACTATGAGAACAGGCAATTTGGCAGAGCTCCTC

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 82.40% 17.60% 0.04% 0.00% NA
All Indica  2759 72.30% 27.60% 0.07% 0.00% NA
All Japonica  1512 99.60% 0.40% 0.00% 0.00% NA
Aus  269 82.20% 17.80% 0.00% 0.00% NA
Indica I  595 69.20% 30.80% 0.00% 0.00% NA
Indica II  465 65.60% 34.40% 0.00% 0.00% NA
Indica III  913 85.80% 14.20% 0.00% 0.00% NA
Indica Intermediate  786 63.10% 36.60% 0.25% 0.00% NA
Temperate Japonica  767 99.50% 0.50% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 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
vg0904455249 A -> T LOC_Os09g08525.1 downstream_gene_variant ; 3391.0bp to feature; MODIFIER silent_mutation Average:47.21; most accessible tissue: Zhenshan97 flower, score: 60.301 N N N N
vg0904455249 A -> T LOC_Os09g08540.1 intron_variant ; MODIFIER silent_mutation Average:47.21; most accessible tissue: Zhenshan97 flower, score: 60.301 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0904455249 1.48E-06 NA mr1208_2 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
vg0904455249 NA 9.78E-08 mr1208_2 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