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Detailed information for vg0233901685:

Variant ID: vg0233901685 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 33901685
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: 268. )

Flanking Sequence (100 bp) in Reference Genome:


AATCCACAAGGGCCTAATAACATGGAGGATATGATTAGTGATATTATGAGGAATAGATTCGGGATTGAAACTAGGAATCATGCTAGAGCTTACAAAAAGC[C/T]
ATATCCTGATTATTATGATAATGTGTCGTTTCCTCGAAATTATAGAGTTCCCGAATTTGCCAAGTTTAGTGGTGAGGATGGTAAGACCACATGGGAGCAT

Reverse complement sequence

ATGCTCCCATGTGGTCTTACCATCCTCACCACTAAACTTGGCAAATTCGGGAACTCTATAATTTCGAGGAAACGACACATTATCATAATAATCAGGATAT[G/A]
GCTTTTTGTAAGCTCTAGCATGATTCCTAGTTTCAATCCCGAATCTATTCCTCATAATATCACTAATCATATCCTCCATGTTATTAGGCCCTTGTGGATT

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 99.70% 0.10% 0.15% 0.00% NA
All Indica  2759 99.50% 0.30% 0.25% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.20% 0.30% 0.50% 0.00% NA
Indica II  465 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 99.60% 0.20% 0.22% 0.00% NA
Indica Intermediate  786 99.60% 0.10% 0.25% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg0233901685 C -> T LOC_Os02g55350.1 missense_variant ; p.Pro233Leu; MODERATE N Average:12.681; most accessible tissue: Callus, score: 27.298 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0233901685 3.03E-06 NA mr1815_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