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Detailed information for vg0334368026:

Variant ID: vg0334368026 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 34368026
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:


AATGTATGAGCGTGCCAGTTGATTTGATCCTATAATCAACAAGAAATAGAGACAAAGAATTCGTGGTTAAATCTATAAATGATAGCCGATCGGCTGGGTG[C/T]
CGATGACATATCATTTATCTTTGAGCCGATGTCATATATGAATCGATCGGCGGTTATAAATAGATAGTAAGGAACTAAATCTATTCGATCGGCTGTAGAT

Reverse complement sequence

ATCTACAGCCGATCGAATAGATTTAGTTCCTTACTATCTATTTATAACCGCCGATCGATTCATATATGACATCGGCTCAAAGATAAATGATATGTCATCG[G/A]
CACCCAGCCGATCGGCTATCATTTATAGATTTAACCACGAATTCTTTGTCTCTATTTCTTGTTGATTATAGGATCAAATCAACTGGCACGCTCATACATT

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 93.30% 6.70% 0.02% 0.00% NA
All Indica  2759 88.50% 11.50% 0.04% 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 67.90% 31.90% 0.17% 0.00% NA
Indica II  465 95.30% 4.70% 0.00% 0.00% NA
Indica III  913 94.20% 5.80% 0.00% 0.00% NA
Indica Intermediate  786 93.40% 6.60% 0.00% 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
vg0334368026 C -> T LOC_Os03g60449.1 upstream_gene_variant ; 3680.0bp to feature; MODIFIER silent_mutation Average:17.354; most accessible tissue: Zhenshan97 panicle, score: 28.447 N N N N
vg0334368026 C -> T LOC_Os03g60440.1 downstream_gene_variant ; 789.0bp to feature; MODIFIER silent_mutation Average:17.354; most accessible tissue: Zhenshan97 panicle, score: 28.447 N N N N
vg0334368026 C -> T LOC_Os03g60440-LOC_Os03g60449 intergenic_region ; MODIFIER silent_mutation Average:17.354; most accessible tissue: Zhenshan97 panicle, score: 28.447 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0334368026 NA 2.80E-06 mr1805 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