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Detailed information for vg0523980909:

Variant ID: vg0523980909 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 23980909
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.81, T: 0.19, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:


ATAAGATATAAATCACACTTAAAGTACTATGAGTGATAAAACATCTCATAGCAAAATAAATTATAATTACATAATTTTTTTTTTGAATAAGACGAATGGT[C/T]
AAACGTGTGAGAAAAAGTCAACGGCGTCATCTATTAAAAAACGGAGGGAGTACATATTTTGAATATGTAATTCGGTTTAGCTTTTCAGTGACATGTAAAA

Reverse complement sequence

TTTTACATGTCACTGAAAAGCTAAACCGAATTACATATTCAAAATATGTACTCCCTCCGTTTTTTAATAGATGACGCCGTTGACTTTTTCTCACACGTTT[G/A]
ACCATTCGTCTTATTCAAAAAAAAAATTATGTAATTATAATTTATTTTGCTATGAGATGTTTTATCACTCATAGTACTTTAAGTGTGATTTATATCTTAT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 57.60% 42.20% 0.19% 0.00% NA
All Indica  2759 93.40% 6.30% 0.33% 0.00% NA
All Japonica  1512 0.60% 99.40% 0.00% 0.00% NA
Aus  269 30.90% 69.10% 0.00% 0.00% NA
Indica I  595 99.50% 0.50% 0.00% 0.00% NA
Indica II  465 93.50% 6.00% 0.43% 0.00% NA
Indica III  913 89.70% 10.10% 0.22% 0.00% NA
Indica Intermediate  786 93.00% 6.40% 0.64% 0.00% NA
Temperate Japonica  767 0.00% 100.00% 0.00% 0.00% NA
Tropical Japonica  504 1.80% 98.20% 0.00% 0.00% NA
Japonica Intermediate  241 0.00% 100.00% 0.00% 0.00% NA
VI/Aromatic  96 2.10% 97.90% 0.00% 0.00% NA
Intermediate  90 57.80% 42.20% 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
vg0523980909 C -> T LOC_Os05g40890.2 downstream_gene_variant ; 1148.0bp to feature; MODIFIER silent_mutation Average:22.972; most accessible tissue: Zhenshan97 panicle, score: 39.652 N N N N
vg0523980909 C -> T LOC_Os05g40890-LOC_Os05g40900 intergenic_region ; MODIFIER silent_mutation Average:22.972; most accessible tissue: Zhenshan97 panicle, score: 39.652 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0523980909 1.46E-06 5.20E-06 mr1084 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
vg0523980909 NA 2.28E-31 mr1037_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