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Detailed information for vg0823805704:

Variant ID: vg0823805704 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 23805704
Reference Allele: CAlternative Allele: A,T
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:


CCTTCATCCCAGTTTAATCGTCCCTATGATTTTTGAGGTTTTCTCAAAATGATCATCATCGAACAAAGTGTCTCTTTGTTTATCTGGAATGTCATGTATG[C/A,T]
AAACATGCGACTAATCAATTAATCCCTATTAGTTCAAATCCATGTAACATTTAAAGTGTGAATTAATTTTTGTTGAACAAGAAGTGATGGAGCACCTTGA

Reverse complement sequence

TCAAGGTGCTCCATCACTTCTTGTTCAACAAAAATTAATTCACACTTTAAATGTTACATGGATTTGAACTAATAGGGATTAATTGATTAGTCGCATGTTT[G/T,A]
CATACATGACATTCCAGATAAACAAAGAGACACTTTGTTCGATGATGATCATTTTGAGAAAACCTCAAAAATCATAGGGACGATTAAACTGGGATGAAGG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 98.40% 1.00% 0.61% 0.00% T: 0.02%
All Indica  2759 99.50% 0.10% 0.40% 0.00% NA
All Japonica  1512 96.10% 2.90% 0.99% 0.00% NA
Aus  269 99.60% 0.00% 0.00% 0.00% T: 0.37%
Indica I  595 99.00% 0.00% 1.01% 0.00% NA
Indica II  465 99.80% 0.00% 0.22% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.20% 0.30% 0.51% 0.00% NA
Temperate Japonica  767 98.30% 0.50% 1.17% 0.00% NA
Tropical Japonica  504 99.20% 0.80% 0.00% 0.00% NA
Japonica Intermediate  241 82.60% 14.90% 2.49% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 96.70% 0.00% 3.33% 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
vg0823805704 C -> T LOC_Os08g37580.1 upstream_gene_variant ; 252.0bp to feature; MODIFIER silent_mutation Average:76.211; most accessible tissue: Zhenshan97 flower, score: 89.409 N N N N
vg0823805704 C -> T LOC_Os08g37590.1 upstream_gene_variant ; 2400.0bp to feature; MODIFIER silent_mutation Average:76.211; most accessible tissue: Zhenshan97 flower, score: 89.409 N N N N
vg0823805704 C -> T LOC_Os08g37580-LOC_Os08g37590 intergenic_region ; MODIFIER silent_mutation Average:76.211; most accessible tissue: Zhenshan97 flower, score: 89.409 N N N N
vg0823805704 C -> A LOC_Os08g37580.1 upstream_gene_variant ; 252.0bp to feature; MODIFIER silent_mutation Average:76.211; most accessible tissue: Zhenshan97 flower, score: 89.409 N N N N
vg0823805704 C -> A LOC_Os08g37590.1 upstream_gene_variant ; 2400.0bp to feature; MODIFIER silent_mutation Average:76.211; most accessible tissue: Zhenshan97 flower, score: 89.409 N N N N
vg0823805704 C -> A LOC_Os08g37580-LOC_Os08g37590 intergenic_region ; MODIFIER silent_mutation Average:76.211; most accessible tissue: Zhenshan97 flower, score: 89.409 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0823805704 5.49E-07 5.49E-07 mr1067_2 Jap_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