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Detailed information for vg0115499545:

Variant ID: vg0115499545 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 15499545
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.95, T: 0.05, others allele: 0.00, population size: 104. )

Flanking Sequence (100 bp) in Reference Genome:


CATACATAAGTGAACTTTAAACTATTTTTTTCTCTTAAATTATTTATCCAAATCATGATCCGATTGCACCATTAAATTTATTGCAATTAAATCTTTAAAA[C/T]
AAGACCACACATGAATATAATCCGATGAACTTTTTTAAGCTTATTATTGAATTATTTTTAATAAATGTTGCACGCTGTTGCACTAAGTATATGGAATTGT

Reverse complement sequence

ACAATTCCATATACTTAGTGCAACAGCGTGCAACATTTATTAAAAATAATTCAATAATAAGCTTAAAAAAGTTCATCGGATTATATTCATGTGTGGTCTT[G/A]
TTTTAAAGATTTAATTGCAATAAATTTAATGGTGCAATCGGATCATGATTTGGATAAATAATTTAAGAGAAAAAAATAGTTTAAAGTTCACTTATGTATG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 73.00% 26.50% 0.49% 0.00% NA
All Indica  2759 57.40% 41.80% 0.76% 0.00% NA
All Japonica  1512 97.70% 2.30% 0.00% 0.00% NA
Aus  269 79.60% 20.40% 0.00% 0.00% NA
Indica I  595 55.10% 43.40% 1.51% 0.00% NA
Indica II  465 88.20% 11.40% 0.43% 0.00% NA
Indica III  913 44.20% 55.10% 0.66% 0.00% NA
Indica Intermediate  786 56.40% 43.10% 0.51% 0.00% NA
Temperate Japonica  767 99.10% 0.90% 0.00% 0.00% NA
Tropical Japonica  504 95.00% 5.00% 0.00% 0.00% NA
Japonica Intermediate  241 98.80% 1.20% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 87.80% 10.00% 2.22% 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
vg0115499545 C -> T LOC_Os01g27770.1 upstream_gene_variant ; 3651.0bp to feature; MODIFIER silent_mutation Average:76.596; most accessible tissue: Callus, score: 97.159 N N N N
vg0115499545 C -> T LOC_Os01g27760.1 downstream_gene_variant ; 3265.0bp to feature; MODIFIER silent_mutation Average:76.596; most accessible tissue: Callus, score: 97.159 N N N N
vg0115499545 C -> T LOC_Os01g27760-LOC_Os01g27770 intergenic_region ; MODIFIER silent_mutation Average:76.596; most accessible tissue: Callus, score: 97.159 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0115499545 5.00E-11 NA mr1519 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
vg0115499545 2.22E-10 6.51E-13 mr1519 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
vg0115499545 2.29E-11 NA mr1519_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
vg0115499545 2.51E-09 5.35E-20 mr1519_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