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Detailed information for vg1216463200:

Variant ID: vg1216463200 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 16463200
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.87, G: 0.13, others allele: 0.00, population size: 78. )

Flanking Sequence (100 bp) in Reference Genome:


TCGTTCGTTGTAATTATTGTGCTCCTCATGGCTGTCCAAGGTAACAATTTATTTCTGCAATTTTTTATGTTGGTAACTACTTCCCTCTCCGTCAAAGGCT[A/G]
CAGTTTTAACCCAAAAATTTGTTCCATGAAGATTGTAATTTTAGAGTGACCTAATTCTTTTCTCTCTAATACTATCTCATCATTTCTTCTCGTTTTAACC

Reverse complement sequence

GGTTAAAACGAGAAGAAATGATGAGATAGTATTAGAGAGAAAAGAATTAGGTCACTCTAAAATTACAATCTTCATGGAACAAATTTTTGGGTTAAAACTG[T/C]
AGCCTTTGACGGAGAGGGAAGTAGTTACCAACATAAAAAATTGCAGAAATAAATTGTTACCTTGGACAGCCATGAGGAGCACAATAATTACAACGAACGA

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 50.00% 36.60% 0.34% 13.14% NA
All Indica  2759 32.80% 53.60% 0.29% 13.30% NA
All Japonica  1512 79.40% 11.80% 0.40% 8.40% NA
Aus  269 62.80% 10.80% 0.37% 26.02% NA
Indica I  595 21.80% 73.80% 0.34% 4.03% NA
Indica II  465 70.50% 20.00% 0.22% 9.25% NA
Indica III  913 16.00% 61.90% 0.11% 22.02% NA
Indica Intermediate  786 38.40% 48.50% 0.51% 12.60% NA
Temperate Japonica  767 91.10% 2.10% 0.52% 6.26% NA
Tropical Japonica  504 62.70% 27.60% 0.20% 9.52% NA
Japonica Intermediate  241 76.80% 10.00% 0.41% 12.86% NA
VI/Aromatic  96 29.20% 15.60% 1.04% 54.17% NA
Intermediate  90 64.40% 30.00% 0.00% 5.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1216463200 A -> DEL N N silent_mutation Average:62.317; most accessible tissue: Minghui63 young leaf, score: 78.821 N N N N
vg1216463200 A -> G LOC_Os12g27920.1 downstream_gene_variant ; 4812.0bp to feature; MODIFIER silent_mutation Average:62.317; most accessible tissue: Minghui63 young leaf, score: 78.821 N N N N
vg1216463200 A -> G LOC_Os12g27930.1 intron_variant ; MODIFIER silent_mutation Average:62.317; most accessible tissue: Minghui63 young leaf, score: 78.821 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1216463200 1.33E-07 NA mr1018 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
vg1216463200 7.79E-06 NA mr1055 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
vg1216463200 1.90E-07 NA mr1132 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
vg1216463200 1.83E-07 NA mr1132 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
vg1216463200 3.74E-07 NA mr1178 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
vg1216463200 3.74E-06 NA mr1178 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
vg1216463200 5.77E-08 NA mr1390 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
vg1216463200 2.72E-07 NA mr1490 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
vg1216463200 1.08E-06 NA mr1055_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
vg1216463200 7.42E-06 NA mr1132_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
vg1216463200 5.84E-06 NA mr1390_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
vg1216463200 7.31E-06 NA mr1390_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
vg1216463200 1.58E-06 NA mr1489_2 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
vg1216463200 NA 6.72E-06 mr1874_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