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Detailed information for vg0809212456:

Variant ID: vg0809212456 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 9212456
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.86, G: 0.14, others allele: 0.00, population size: 58. )

Flanking Sequence (100 bp) in Reference Genome:


TAAATATAAATCGGGGTGGATTTTTATCATCCGCATGTGAAAATCAATTTTTCCAGGCGGACCACTTAAGGGGTTCGCCTGCGAAAATATATTTATTTTC[A/G]
CAGGTGGACCCCTTAAGTGGTCCGTTTGAAAAAATATGATTTTTCTGGGCGGAACCTTATATATAGTCCGCCTGCAAAAATGTCAAAAAAAAAAATCTTC

Reverse complement sequence

GAAGATTTTTTTTTTTGACATTTTTGCAGGCGGACTATATATAAGGTTCCGCCCAGAAAAATCATATTTTTTCAAACGGACCACTTAAGGGGTCCACCTG[T/C]
GAAAATAAATATATTTTCGCAGGCGAACCCCTTAAGTGGTCCGCCTGGAAAAATTGATTTTCACATGCGGATGATAAAAATCCACCCCGATTTATATTTA

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 58.90% 39.70% 0.51% 0.91% NA
All Indica  2759 71.40% 27.60% 0.29% 0.72% NA
All Japonica  1512 42.30% 55.40% 0.86% 1.52% NA
Aus  269 42.40% 57.20% 0.37% 0.00% NA
Indica I  595 80.00% 19.30% 0.17% 0.50% NA
Indica II  465 22.20% 74.40% 0.65% 2.80% NA
Indica III  913 92.30% 7.30% 0.11% 0.22% NA
Indica Intermediate  786 69.70% 29.60% 0.38% 0.25% NA
Temperate Japonica  767 58.70% 39.10% 0.91% 1.30% NA
Tropical Japonica  504 21.60% 76.00% 0.60% 1.79% NA
Japonica Intermediate  241 33.20% 63.90% 1.24% 1.66% NA
VI/Aromatic  96 11.50% 88.50% 0.00% 0.00% NA
Intermediate  90 53.30% 44.40% 2.22% 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
vg0809212456 A -> G LOC_Os08g15220.1 upstream_gene_variant ; 890.0bp to feature; MODIFIER silent_mutation Average:65.193; most accessible tissue: Minghui63 young leaf, score: 76.385 N N N N
vg0809212456 A -> G LOC_Os08g15204-LOC_Os08g15220 intergenic_region ; MODIFIER silent_mutation Average:65.193; most accessible tissue: Minghui63 young leaf, score: 76.385 N N N N
vg0809212456 A -> DEL N N silent_mutation Average:65.193; most accessible tissue: Minghui63 young leaf, score: 76.385 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0809212456 NA 2.15E-06 mr1090 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
vg0809212456 NA 9.47E-08 mr1133 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
vg0809212456 NA 6.85E-08 mr1090_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
vg0809212456 NA 7.60E-07 mr1323_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
vg0809212456 NA 4.51E-08 mr1330_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
vg0809212456 NA 3.10E-07 mr1360_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
vg0809212456 NA 3.17E-06 mr1448_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
vg0809212456 NA 3.05E-06 mr1449_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
vg0809212456 NA 5.36E-07 mr1540_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
vg0809212456 NA 2.29E-08 mr1553_2 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
vg0809212456 NA 2.02E-09 mr1715_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
vg0809212456 NA 1.67E-07 mr1732_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
vg0809212456 NA 3.44E-06 mr1994_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