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Detailed information for vg0208593323:

Variant ID: vg0208593323 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 8593323
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.00, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:


GTTGATTTCTTTCGAAACTTTTACAAGTAATTGAACCATAGACCGAGCAAAAGAAACAAATCGATTTGAGATCATGCTAGCTGAACACCACCCTAGAATC[C/T]
TAGATATATAGGTAGATGGTGCTGGACTATGAATTTTTGTACGCATACCAAGATCGATCCATAGCTAGATATATAGGAACCCATATGTGTTCATGTAGAT

Reverse complement sequence

ATCTACATGAACACATATGGGTTCCTATATATCTAGCTATGGATCGATCTTGGTATGCGTACAAAAATTCATAGTCCAGCACCATCTACCTATATATCTA[G/A]
GATTCTAGGGTGGTGTTCAGCTAGCATGATCTCAAATCGATTTGTTTCTTTTGCTCGGTCTATGGTTCAATTACTTGTAAAAGTTTCGAAAGAAATCAAC

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 87.60% 12.30% 0.04% 0.00% NA
All Indica  2759 81.90% 18.10% 0.04% 0.00% NA
All Japonica  1512 99.50% 0.50% 0.00% 0.00% NA
Aus  269 75.50% 24.20% 0.37% 0.00% NA
Indica I  595 79.50% 20.30% 0.17% 0.00% NA
Indica II  465 64.90% 35.10% 0.00% 0.00% NA
Indica III  913 90.50% 9.50% 0.00% 0.00% NA
Indica Intermediate  786 83.80% 16.20% 0.00% 0.00% NA
Temperate Japonica  767 99.30% 0.70% 0.00% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 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 87.80% 12.20% 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
vg0208593323 C -> T LOC_Os02g15360.1 downstream_gene_variant ; 3844.0bp to feature; MODIFIER silent_mutation Average:35.273; most accessible tissue: Callus, score: 82.117 N N N N
vg0208593323 C -> T LOC_Os02g15350.1 intron_variant ; MODIFIER silent_mutation Average:35.273; most accessible tissue: Callus, score: 82.117 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0208593323 NA 7.30E-06 mr1293 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
vg0208593323 NA 7.77E-06 mr1507 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
vg0208593323 NA 5.74E-06 mr1508 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
vg0208593323 NA 2.84E-07 mr1884 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