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Detailed information for vg0417267842:

Variant ID: vg0417267842 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 17267842
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.84, T: 0.16, others allele: 0.00, population size: 43. )

Flanking Sequence (100 bp) in Reference Genome:


AACCTGAATTTAGGAAGAAATCTTTAAATGGGGGGAGAAACAGGTTAGCTGGAGGTGATACAGTATACCAATGCGGCGGGTCGCGAGGCTTGGTTGCTAC[G/T]
AAACTGTACCTGGTGCTTGTTAATTTGTAGCAATTCATAGGGCTTGTTCCTATATAAAATCGTTGCATATACTAATTTATTTGTAATGTAGCAACATAAA

Reverse complement sequence

TTTATGTTGCTACATTACAAATAAATTAGTATATGCAACGATTTTATATAGGAACAAGCCCTATGAATTGCTACAAATTAACAAGCACCAGGTACAGTTT[C/A]
GTAGCAACCAAGCCTCGCGACCCGCCGCATTGGTATACTGTATCACCTCCAGCTAACCTGTTTCTCCCCCCATTTAAAGATTTCTTCCTAAATTCAGGTT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 87.80% 12.10% 0.11% 0.00% NA
All Indica  2759 94.80% 5.20% 0.00% 0.00% NA
All Japonica  1512 75.00% 24.70% 0.33% 0.00% NA
Aus  269 97.00% 3.00% 0.00% 0.00% NA
Indica I  595 79.70% 20.30% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 99.10% 0.90% 0.00% 0.00% NA
Indica Intermediate  786 98.30% 1.70% 0.00% 0.00% NA
Temperate Japonica  767 57.90% 41.50% 0.65% 0.00% NA
Tropical Japonica  504 99.20% 0.80% 0.00% 0.00% NA
Japonica Intermediate  241 78.80% 21.20% 0.00% 0.00% NA
VI/Aromatic  96 60.40% 39.60% 0.00% 0.00% NA
Intermediate  90 91.10% 8.90% 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
vg0417267842 G -> T LOC_Os04g29090.1 upstream_gene_variant ; 4710.0bp to feature; MODIFIER silent_mutation Average:48.261; most accessible tissue: Zhenshan97 young leaf, score: 65.28 N N N N
vg0417267842 G -> T LOC_Os04g29100.1 upstream_gene_variant ; 1198.0bp to feature; MODIFIER silent_mutation Average:48.261; most accessible tissue: Zhenshan97 young leaf, score: 65.28 N N N N
vg0417267842 G -> T LOC_Os04g29090-LOC_Os04g29100 intergenic_region ; MODIFIER silent_mutation Average:48.261; most accessible tissue: Zhenshan97 young leaf, score: 65.28 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0417267842 5.77E-07 NA mr1137_2 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
vg0417267842 6.66E-08 NA mr1617_2 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