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Detailed information for vg0431397443:

Variant ID: vg0431397443 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 31397443
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, A: 0.03, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:


ATCTTGGAAAGGAAGAGCGATATGCATAGCACCTAAACCCCAGCTTTGTGTGTGTTTATGCAGTAGAGGTTTGAGTTATTTATGAAGATACTTTCTTTAT[C/A]
CAATGCTAACACACTAGGACACGTATCGACCATGGGAGGTGGGACTTGGCATTTTATAAAAAAGAAGAAGAGAAGTTTGGCCAAGTTCATTCAACCATCT

Reverse complement sequence

AGATGGTTGAATGAACTTGGCCAAACTTCTCTTCTTCTTTTTTATAAAATGCCAAGTCCCACCTCCCATGGTCGATACGTGTCCTAGTGTGTTAGCATTG[G/T]
ATAAAGAAAGTATCTTCATAAATAACTCAAACCTCTACTGCATAAACACACACAAAGCTGGGGTTTAGGTGCTATGCATATCGCTCTTCCTTTCCAAGAT

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 91.00% 8.80% 0.13% 0.00% NA
All Indica  2759 86.90% 12.90% 0.22% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 81.00% 19.00% 0.00% 0.00% NA
Indica I  595 97.30% 2.70% 0.00% 0.00% NA
Indica II  465 94.60% 5.40% 0.00% 0.00% NA
Indica III  913 76.20% 23.30% 0.44% 0.00% NA
Indica Intermediate  786 86.80% 13.00% 0.25% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 90.00% 10.00% 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
vg0431397443 C -> A LOC_Os04g52720.1 upstream_gene_variant ; 2258.0bp to feature; MODIFIER silent_mutation Average:59.475; most accessible tissue: Zhenshan97 flower, score: 84.018 N N N N
vg0431397443 C -> A LOC_Os04g52725.1 upstream_gene_variant ; 1255.0bp to feature; MODIFIER silent_mutation Average:59.475; most accessible tissue: Zhenshan97 flower, score: 84.018 N N N N
vg0431397443 C -> A LOC_Os04g52710.1 downstream_gene_variant ; 3448.0bp to feature; MODIFIER silent_mutation Average:59.475; most accessible tissue: Zhenshan97 flower, score: 84.018 N N N N
vg0431397443 C -> A LOC_Os04g52710.2 downstream_gene_variant ; 3448.0bp to feature; MODIFIER silent_mutation Average:59.475; most accessible tissue: Zhenshan97 flower, score: 84.018 N N N N
vg0431397443 C -> A LOC_Os04g52710.3 downstream_gene_variant ; 3448.0bp to feature; MODIFIER silent_mutation Average:59.475; most accessible tissue: Zhenshan97 flower, score: 84.018 N N N N
vg0431397443 C -> A LOC_Os04g52720-LOC_Os04g52725 intergenic_region ; MODIFIER silent_mutation Average:59.475; most accessible tissue: Zhenshan97 flower, score: 84.018 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0431397443 7.76E-06 8.88E-06 mr1138 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
vg0431397443 NA 8.61E-06 mr1138_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