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Detailed information for vg0724693113:

Variant ID: vg0724693113 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 24693113
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

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

Flanking Sequence (100 bp) in Reference Genome:


ATCTACCCAATGGCACGCTTAGAGGTCAATAATAGGACTTTAATTTTGCCGTTTGTTGAGTCGTCTCGTTCGCGTGTAGCTTCGGAGCTCGAAGACCCGG[A/T]
GTGCGCGGATTTCGAGGATCAAGCTCAAGATCTCGAGCAAGGCAAGTCACCTTTGATCATCTTGCACCTATTATTTAAATCTAAATATTTCTTTTCCGCA

Reverse complement sequence

TGCGGAAAAGAAATATTTAGATTTAAATAATAGGTGCAAGATGATCAAAGGTGACTTGCCTTGCTCGAGATCTTGAGCTTGATCCTCGAAATCCGCGCAC[T/A]
CCGGGTCTTCGAGCTCCGAAGCTACACGCGAACGAGACGACTCAACAAACGGCAAAATTAAAGTCCTATTATTGACCTCTAAGCGTGCCATTGGGTAGAT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 84.30% 2.80% 12.23% 0.66% NA
All Indica  2759 74.70% 4.30% 19.90% 1.12% NA
All Japonica  1512 99.70% 0.10% 0.13% 0.00% NA
Aus  269 96.70% 0.00% 3.35% 0.00% NA
Indica I  595 99.70% 0.00% 0.34% 0.00% NA
Indica II  465 65.20% 6.00% 28.17% 0.65% NA
Indica III  913 62.00% 5.80% 29.79% 2.41% NA
Indica Intermediate  786 76.20% 4.70% 18.32% 0.76% NA
Temperate Japonica  767 99.60% 0.30% 0.13% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.00% 0.41% 0.00% NA
VI/Aromatic  96 80.20% 10.40% 9.38% 0.00% NA
Intermediate  90 86.70% 3.30% 10.00% 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
vg0724693113 A -> DEL N N silent_mutation Average:28.011; most accessible tissue: Zhenshan97 flower, score: 39.624 N N N N
vg0724693113 A -> T LOC_Os07g41220-LOC_Os07g41230 intergenic_region ; MODIFIER silent_mutation Average:28.011; most accessible tissue: Zhenshan97 flower, score: 39.624 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0724693113 9.49E-06 NA mr1120 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
vg0724693113 7.38E-07 2.87E-08 mr1120 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
vg0724693113 NA 2.07E-07 mr1120_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
vg0724693113 NA 2.30E-06 mr1247_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