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Detailed information for vg1216529599:

Variant ID: vg1216529599 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 16529599
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:


AATGGTTGGGGCTCTTTGTTGCCAAGCAAATTGCTTCAACACTGCTATCATGCAACACATAGGAAGGATGCAAATGCAGCAAGAAGCTATACAGGGTGTC[A/G]
GTACTTGTTTATTACACTTCATTTGGTGGTTTTAATTTCTATCATTAAAGAGTTCGAGCAGCCACAGGGTTTCAAAAGGATTACTTCATTGGCTTGTGGT

Reverse complement sequence

ACCACAAGCCAATGAAGTAATCCTTTTGAAACCCTGTGGCTGCTCGAACTCTTTAATGATAGAAATTAAAACCACCAAATGAAGTGTAATAAACAAGTAC[T/C]
GACACCCTGTATAGCTTCTTGCTGCATTTGCATCCTTCCTATGTGTTGCATGATAGCAGTGTTGAAGCAATTTGCTTGGCAACAAAGAGCCCCAACCATT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 48.80% 9.20% 3.20% 38.74% NA
All Indica  2759 48.50% 0.70% 1.41% 49.44% NA
All Japonica  1512 47.90% 26.90% 7.01% 18.19% NA
Aus  269 48.00% 0.00% 0.00% 52.04% NA
Indica I  595 35.30% 0.20% 1.34% 63.19% NA
Indica II  465 19.60% 2.20% 2.37% 75.91% NA
Indica III  913 77.10% 0.00% 0.33% 22.56% NA
Indica Intermediate  786 42.20% 1.00% 2.16% 54.58% NA
Temperate Japonica  767 37.90% 48.80% 12.26% 1.04% NA
Tropical Japonica  504 50.00% 0.60% 0.40% 49.01% NA
Japonica Intermediate  241 75.10% 12.40% 4.15% 8.30% NA
VI/Aromatic  96 75.00% 0.00% 0.00% 25.00% NA
Intermediate  90 50.00% 12.20% 6.67% 31.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1216529599 A -> DEL N N silent_mutation Average:9.426; most accessible tissue: Callus, score: 33.338 N N N N
vg1216529599 A -> G LOC_Os12g28020.1 intron_variant ; MODIFIER silent_mutation Average:9.426; most accessible tissue: Callus, score: 33.338 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1216529599 NA 1.87E-08 mr1002 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
vg1216529599 NA 7.19E-09 mr1137 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
vg1216529599 NA 3.79E-07 mr1163 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
vg1216529599 4.88E-07 NA mr1670 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
vg1216529599 NA 3.76E-10 mr1002_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
vg1216529599 NA 7.62E-08 mr1137_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
vg1216529599 NA 2.10E-06 mr1182_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