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Detailed information for vg1015565858:

Variant ID: vg1015565858 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 15565858
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 295. )

Flanking Sequence (100 bp) in Reference Genome:


GGAACTAAGCTTTATTACATAGGAATTTAAACTGCAATTGTTCTGATCTGAATTAAAACACTTAAAAAGCAAGCAAAAATCCTTATTAAGACAGCCATAT[C/T]
ATAGGCACATGATATCGACCGTCGACTGACCCACAAGCAAGCAACCTAGACACACAAACTAACAAACAAAAGCTAGACAGTCGATAAACTAATGGAAAAC

Reverse complement sequence

GTTTTCCATTAGTTTATCGACTGTCTAGCTTTTGTTTGTTAGTTTGTGTGTCTAGGTTGCTTGCTTGTGGGTCAGTCGACGGTCGATATCATGTGCCTAT[G/A]
ATATGGCTGTCTTAATAAGGATTTTTGCTTGCTTTTTAAGTGTTTTAATTCAGATCAGAACAATTGCAGTTTAAATTCCTATGTAATAAAGCTTAGTTCC

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 98.10% 0.40% 0.25% 1.31% NA
All Indica  2759 99.20% 0.60% 0.14% 0.00% NA
All Japonica  1512 95.40% 0.00% 0.53% 4.10% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.20% 0.80% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.10% 0.70% 0.22% 0.00% NA
Indica Intermediate  786 99.00% 0.80% 0.25% 0.00% NA
Temperate Japonica  767 91.00% 0.00% 1.04% 7.95% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.00% 0.00% 0.41% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg1015565858 C -> T LOC_Os10g29980.1 upstream_gene_variant ; 147.0bp to feature; MODIFIER silent_mutation Average:23.864; most accessible tissue: Minghui63 panicle, score: 42.799 N N N N
vg1015565858 C -> T LOC_Os10g29990.1 downstream_gene_variant ; 105.0bp to feature; MODIFIER silent_mutation Average:23.864; most accessible tissue: Minghui63 panicle, score: 42.799 N N N N
vg1015565858 C -> T LOC_Os10g29980-LOC_Os10g29990 intergenic_region ; MODIFIER silent_mutation Average:23.864; most accessible tissue: Minghui63 panicle, score: 42.799 N N N N
vg1015565858 C -> DEL N N silent_mutation Average:23.864; most accessible tissue: Minghui63 panicle, score: 42.799 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1015565858 1.88E-06 1.56E-07 mr1874 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