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Detailed information for vg0234915674:

Variant ID: vg0234915674 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 34915674
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 331. )

Flanking Sequence (100 bp) in Reference Genome:


CAATCAGTTCCATAGTTCATATCCTCTTGGAACTGCAGTCCGTCTAATATGTTTGCAAATACTATGGTTGCTCCTCTTAACTAATCTAGCAGAAATCCAG[C/A]
AGAAATTGCATTTGCATTTGTTCGAAAAGTGATATCCCTGAACACATGTTAGTAAAAGTTTAACCACAGTCTGTTGCACAACCAGGTACAAGGTCAAATA

Reverse complement sequence

TATTTGACCTTGTACCTGGTTGTGCAACAGACTGTGGTTAAACTTTTACTAACATGTGTTCAGGGATATCACTTTTCGAACAAATGCAAATGCAATTTCT[G/T]
CTGGATTTCTGCTAGATTAGTTAAGAGGAGCAACCATAGTATTTGCAAACATATTAGACGGACTGCAGTTCCAAGAGGATATGAACTATGGAACTGATTG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 96.20% 2.70% 1.10% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 88.20% 8.40% 3.44% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 77.80% 15.80% 6.39% 0.00% NA
Tropical Japonica  504 99.60% 0.00% 0.40% 0.00% NA
Japonica Intermediate  241 97.10% 2.50% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 97.80% 2.20% 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
vg0234915674 C -> A LOC_Os02g56950.1 upstream_gene_variant ; 4852.0bp to feature; MODIFIER silent_mutation Average:62.838; most accessible tissue: Minghui63 flower, score: 78.041 N N N N
vg0234915674 C -> A LOC_Os02g56990.1 upstream_gene_variant ; 2437.0bp to feature; MODIFIER silent_mutation Average:62.838; most accessible tissue: Minghui63 flower, score: 78.041 N N N N
vg0234915674 C -> A LOC_Os02g57000.1 upstream_gene_variant ; 4868.0bp to feature; MODIFIER silent_mutation Average:62.838; most accessible tissue: Minghui63 flower, score: 78.041 N N N N
vg0234915674 C -> A LOC_Os02g56950.2 upstream_gene_variant ; 4852.0bp to feature; MODIFIER silent_mutation Average:62.838; most accessible tissue: Minghui63 flower, score: 78.041 N N N N
vg0234915674 C -> A LOC_Os02g56960.1 downstream_gene_variant ; 2150.0bp to feature; MODIFIER silent_mutation Average:62.838; most accessible tissue: Minghui63 flower, score: 78.041 N N N N
vg0234915674 C -> A LOC_Os02g56970.1 downstream_gene_variant ; 188.0bp to feature; MODIFIER silent_mutation Average:62.838; most accessible tissue: Minghui63 flower, score: 78.041 N N N N
vg0234915674 C -> A LOC_Os02g56980.1 downstream_gene_variant ; 117.0bp to feature; MODIFIER silent_mutation Average:62.838; most accessible tissue: Minghui63 flower, score: 78.041 N N N N
vg0234915674 C -> A LOC_Os02g56970-LOC_Os02g56980 intergenic_region ; MODIFIER silent_mutation Average:62.838; most accessible tissue: Minghui63 flower, score: 78.041 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0234915674 2.57E-06 2.57E-06 mr1004_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