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Detailed information for vg0815688233:

Variant ID: vg0815688233 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 15688233
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.80, T: 0.21, others allele: 0.00, population size: 227. )

Flanking Sequence (100 bp) in Reference Genome:


TGCATCTCTCGACTGTAAAACCGGATAGATCGTCCTCCAACTATTAAAATTTAAAACCAATGTAAATATAGTCCTTCAGCAGTGCGGAGCACGGTTTTGT[C/T]
GTATGTGGTGCTAATGTAGCGTTATAAAAAAAGAATTCGTGGGTCCCAGCAGTAAGTAAAACGTTGATATTTTTCTTACTCTCATGCCTCCTCCCTAATA

Reverse complement sequence

TATTAGGGAGGAGGCATGAGAGTAAGAAAAATATCAACGTTTTACTTACTGCTGGGACCCACGAATTCTTTTTTTATAACGCTACATTAGCACCACATAC[G/A]
ACAAAACCGTGCTCCGCACTGCTGAAGGACTATATTTACATTGGTTTTAAATTTTAATAGTTGGAGGACGATCTATCCGGTTTTACAGTCGAGAGATGCA

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 61.50% 38.50% 0.02% 0.00% NA
All Indica  2759 93.70% 6.20% 0.04% 0.00% NA
All Japonica  1512 6.30% 93.70% 0.00% 0.00% NA
Aus  269 71.00% 29.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 95.30% 4.70% 0.00% 0.00% NA
Indica III  913 91.70% 8.30% 0.00% 0.00% NA
Indica Intermediate  786 90.50% 9.40% 0.13% 0.00% NA
Temperate Japonica  767 9.90% 90.10% 0.00% 0.00% NA
Tropical Japonica  504 2.40% 97.60% 0.00% 0.00% NA
Japonica Intermediate  241 2.90% 97.10% 0.00% 0.00% NA
VI/Aromatic  96 3.10% 96.90% 0.00% 0.00% NA
Intermediate  90 35.60% 64.40% 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
vg0815688233 C -> T LOC_Os08g25780.1 upstream_gene_variant ; 2039.0bp to feature; MODIFIER silent_mutation Average:75.411; most accessible tissue: Callus, score: 92.947 N N N N
vg0815688233 C -> T LOC_Os08g25770.1 intron_variant ; MODIFIER silent_mutation Average:75.411; most accessible tissue: Callus, score: 92.947 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0815688233 NA 6.80E-07 mr1510 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
vg0815688233 NA 5.67E-11 mr1713 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
vg0815688233 NA 9.77E-06 mr1932 Ind_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
vg0815688233 NA 4.37E-07 mr1134_2 Ind_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
vg0815688233 2.54E-07 5.20E-10 mr1672_2 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