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Detailed information for vg0816379171:

Variant ID: vg0816379171 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 16379171
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: 122. )

Flanking Sequence (100 bp) in Reference Genome:


TTTGACTTTTAGTTTTATTAAATTAATAATTAAATATATTTTTATAATAAATTTATCTTGGTCAAAAATATTATTATTATTTTCTATAAACTTGGTCAAA[C/T]
TTGAGGTAGTTTGACTTCGATCAAAGTCAAAACATATTATAACTTGAAATGGAGGGAGTAATTTCTTATTTCTATTATTATTTTTCTTTCTTTCACCCTA

Reverse complement sequence

TAGGGTGAAAGAAAGAAAAATAATAATAGAAATAAGAAATTACTCCCTCCATTTCAAGTTATAATATGTTTTGACTTTGATCGAAGTCAAACTACCTCAA[G/A]
TTTGACCAAGTTTATAGAAAATAATAATAATATTTTTGACCAAGATAAATTTATTATAAAAATATATTTAATTATTAATTTAATAAAACTAAAAGTCAAA

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 55.90% 43.80% 0.36% 0.00% NA
All Indica  2759 26.10% 73.40% 0.51% 0.00% NA
All Japonica  1512 98.80% 1.10% 0.07% 0.00% NA
Aus  269 99.30% 0.70% 0.00% 0.00% NA
Indica I  595 33.80% 65.90% 0.34% 0.00% NA
Indica II  465 8.80% 91.00% 0.22% 0.00% NA
Indica III  913 32.20% 67.40% 0.44% 0.00% NA
Indica Intermediate  786 23.50% 75.60% 0.89% 0.00% NA
Temperate Japonica  767 99.00% 1.00% 0.00% 0.00% NA
Tropical Japonica  504 99.00% 1.00% 0.00% 0.00% NA
Japonica Intermediate  241 97.90% 1.70% 0.41% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 71.10% 26.70% 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
vg0816379171 C -> T LOC_Os08g26880.1 downstream_gene_variant ; 4801.0bp to feature; MODIFIER silent_mutation Average:20.589; most accessible tissue: Callus, score: 31.178 N N N N
vg0816379171 C -> T LOC_Os08g26880-LOC_Os08g26890 intergenic_region ; MODIFIER silent_mutation Average:20.589; most accessible tissue: Callus, score: 31.178 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0816379171 NA 8.19E-07 mr1040 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
vg0816379171 NA 7.56E-07 mr1321 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
vg0816379171 1.74E-06 1.82E-06 mr1349 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
vg0816379171 NA 2.03E-10 mr1581 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
vg0816379171 NA 3.09E-07 mr1527_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