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Detailed information for vg0228010095:

Variant ID: vg0228010095 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 28010095
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: 313. )

Flanking Sequence (100 bp) in Reference Genome:


TTGATGCAAGACCTAGCGGTGGGACAATGAAAACGACTGACGGCAGGAGCTCGGTGCAAAGGGAGCCACGGAGACTGACGTCAGGGTCTATTGGGTGGGA[C/T]
GACAGTTGGATGTGCACAGCCTGTGTGCCACACTGGTCGTGCACCACCTTTCCACGGGTCGAGGATTGGAGGATATGCATGCCAGTGCCATGAACAGTGA

Reverse complement sequence

TCACTGTTCATGGCACTGGCATGCATATCCTCCAATCCTCGACCCGTGGAAAGGTGGTGCACGACCAGTGTGGCACACAGGCTGTGCACATCCAACTGTC[G/A]
TCCCACCCAATAGACCCTGACGTCAGTCTCCGTGGCTCCCTTTGCACCGAGCTCCTGCCGTCAGTCGTTTTCATTGTCCCACCGCTAGGTCTTGCATCAA

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 95.90% 2.70% 1.38% 0.00% NA
All Indica  2759 99.60% 0.30% 0.04% 0.00% NA
All Japonica  1512 88.20% 7.70% 4.17% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.80% 0.00% 0.17% 0.00% NA
Indica II  465 99.40% 0.60% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.20% 0.80% 0.00% 0.00% NA
Temperate Japonica  767 78.90% 14.70% 6.39% 0.00% NA
Tropical Japonica  504 99.00% 0.40% 0.60% 0.00% NA
Japonica Intermediate  241 95.00% 0.40% 4.56% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 95.60% 3.30% 1.11% 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
vg0228010095 C -> T LOC_Os02g45980.1 upstream_gene_variant ; 4727.0bp to feature; MODIFIER silent_mutation Average:75.975; most accessible tissue: Zhenshan97 young leaf, score: 89.666 N N N N
vg0228010095 C -> T LOC_Os02g45960.1 downstream_gene_variant ; 3717.0bp to feature; MODIFIER silent_mutation Average:75.975; most accessible tissue: Zhenshan97 young leaf, score: 89.666 N N N N
vg0228010095 C -> T LOC_Os02g45974.1 downstream_gene_variant ; 2716.0bp to feature; MODIFIER silent_mutation Average:75.975; most accessible tissue: Zhenshan97 young leaf, score: 89.666 N N N N
vg0228010095 C -> T LOC_Os02g45960-LOC_Os02g45974 intergenic_region ; MODIFIER silent_mutation Average:75.975; most accessible tissue: Zhenshan97 young leaf, score: 89.666 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0228010095 NA 2.45E-06 mr1332_2 Jap_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
vg0228010095 1.19E-07 9.65E-10 mr1588_2 Jap_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