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Detailed information for vg0814903603:

Variant ID: vg0814903603 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 14903603
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 295. )

Flanking Sequence (100 bp) in Reference Genome:


ATCGAAAACCTAAACAAAAGACCAAAAGAAAGATCCTATTTAGACTAATTAGTAGTGCCATTAGATAGATCTTAATTTTACGGAATTACTGGAAGTTGAA[C/T]
GGAGTCAAACGAAGCTATGGATCGAGAGATATGAATTTTGGAAGTTTAAATGGATTTTCTGGACGAGAAATGATTTATCGGAATTTATAGAAATAATATT

Reverse complement sequence

AATATTATTTCTATAAATTCCGATAAATCATTTCTCGTCCAGAAAATCCATTTAAACTTCCAAAATTCATATCTCTCGATCCATAGCTTCGTTTGACTCC[G/A]
TTCAACTTCCAGTAATTCCGTAAAATTAAGATCTATCTAATGGCACTACTAATTAGTCTAAATAGGATCTTTCTTTTGGTCTTTTGTTTAGGTTTTCGAT

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 86.50% 13.30% 0.19% 0.00% NA
All Indica  2759 99.80% 0.20% 0.00% 0.00% NA
All Japonica  1512 58.90% 40.50% 0.60% 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 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 99.80% 0.20% 0.00% 0.00% NA
Indica Intermediate  786 99.70% 0.30% 0.00% 0.00% NA
Temperate Japonica  767 47.50% 51.60% 0.91% 0.00% NA
Tropical Japonica  504 72.00% 27.60% 0.40% 0.00% NA
Japonica Intermediate  241 68.00% 32.00% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 88.90% 11.10% 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
vg0814903603 C -> T LOC_Os08g24650.1 upstream_gene_variant ; 1105.0bp to feature; MODIFIER silent_mutation Average:23.804; most accessible tissue: Zhenshan97 flag leaf, score: 42.807 N N N N
vg0814903603 C -> T LOC_Os08g24660.1 upstream_gene_variant ; 1216.0bp to feature; MODIFIER silent_mutation Average:23.804; most accessible tissue: Zhenshan97 flag leaf, score: 42.807 N N N N
vg0814903603 C -> T LOC_Os08g24650-LOC_Os08g24660 intergenic_region ; MODIFIER silent_mutation Average:23.804; most accessible tissue: Zhenshan97 flag leaf, score: 42.807 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0814903603 1.73E-09 6.02E-12 mr1708 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
vg0814903603 9.01E-08 2.32E-09 mr1708 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