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Detailed information for vg0414482821:

Variant ID: vg0414482821 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 14482821
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.70, A: 0.30, others allele: 0.00, population size: 100. )

Flanking Sequence (100 bp) in Reference Genome:


GCAATGGTGCGCGGCGGGGGCAAACCAGAGCTTTGTGGTTAGGACATGGGAAAGATGGTGGGATGTGCCGTAGAGAAAAAAGGGAACCGGTGATTGACCC[A/G]
GGCGACCCTTGGTTCCAAATATATAATGTGTATTTTCTCTAAAACATAAGGGAACAAGGGTAGGATGGCTAGAGCTAACCGCTCTCAACGCATAGATCCC

Reverse complement sequence

GGGATCTATGCGTTGAGAGCGGTTAGCTCTAGCCATCCTACCCTTGTTCCCTTATGTTTTAGAGAAAATACACATTATATATTTGGAACCAAGGGTCGCC[T/C]
GGGTCAATCACCGGTTCCCTTTTTTCTCTACGGCACATCCCACCATCTTTCCCATGTCCTAACCACAAAGCTCTGGTTTGCCCCCGCCGCGCACCATTGC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 42.20% 36.50% 9.59% 11.76% NA
All Indica  2759 26.60% 48.20% 12.40% 12.79% NA
All Japonica  1512 78.90% 4.20% 5.49% 11.44% NA
Aus  269 0.40% 98.10% 0.74% 0.74% NA
Indica I  595 33.40% 31.30% 15.63% 19.66% NA
Indica II  465 11.00% 82.40% 3.66% 3.01% NA
Indica III  913 32.00% 36.10% 15.55% 16.32% NA
Indica Intermediate  786 24.60% 54.70% 11.45% 9.29% NA
Temperate Japonica  767 87.00% 1.70% 2.09% 9.26% NA
Tropical Japonica  504 78.20% 4.40% 5.16% 12.30% NA
Japonica Intermediate  241 54.80% 11.60% 17.01% 16.60% NA
VI/Aromatic  96 24.00% 35.40% 19.79% 20.83% NA
Intermediate  90 46.70% 36.70% 7.78% 8.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0414482821 A -> DEL N N silent_mutation Average:17.253; most accessible tissue: Callus, score: 55.535 N N N N
vg0414482821 A -> G LOC_Os04g25080-LOC_Os04g25100 intergenic_region ; MODIFIER silent_mutation Average:17.253; most accessible tissue: Callus, score: 55.535 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0414482821 3.47E-06 6.72E-26 mr1024_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
vg0414482821 2.10E-06 2.10E-06 mr1024_2 Jap_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
vg0414482821 NA 1.13E-06 mr1275_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
vg0414482821 NA 1.46E-07 mr1681_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
vg0414482821 NA 1.14E-08 mr1940_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