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Detailed information for vg0716355931:

Variant ID: vg0716355931 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 16355931
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:


TTTGCATGCATCCAAAAGACCTTTTTGTTTTCTACAAGTTGAGCAAGAAAACACCTCATCTTGTTTAACAATTTCTTCCATGTGATTAACACGCTCTAAA[G/T]
CATCTTTCAACTTCAACTCATTCAAACCACACTTTGAACAATATTGAGAAATCAAAGCACCATTGTTTTGTTTTGCCTTATTTGCACATGAAACATTGAC

Reverse complement sequence

GTCAATGTTTCATGTGCAAATAAGGCAAAACAAAACAATGGTGCTTTGATTTCTCAATATTGTTCAAAGTGTGGTTTGAATGAGTTGAAGTTGAAAGATG[C/A]
TTTAGAGCGTGTTAATCACATGGAAGAAATTGTTAAACAAGATGAGGTGTTTTCTTGCTCAACTTGTAGAAAACAAAAAGGTCTTTTGGATGCATGCAAA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 91.90% 7.60% 0.57% 0.00% NA
All Indica  2759 99.60% 0.40% 0.00% 0.00% NA
All Japonica  1512 76.10% 22.30% 1.59% 0.00% NA
Aus  269 99.30% 0.40% 0.37% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.40% 0.60% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 99.20% 0.80% 0.00% 0.00% NA
Temperate Japonica  767 95.80% 3.30% 0.91% 0.00% NA
Tropical Japonica  504 41.90% 55.00% 3.17% 0.00% NA
Japonica Intermediate  241 85.10% 14.50% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 86.70% 11.10% 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
vg0716355931 G -> T LOC_Os07g28050.1 missense_variant ; p.Ala858Asp; MODERATE nonsynonymous_codon ; A858D Average:20.714; most accessible tissue: Minghui63 flag leaf, score: 29.435 probably damaging 2.068 DELETERIOUS 0.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0716355931 NA 2.37E-06 mr1248 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
vg0716355931 NA 4.36E-07 mr1554 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
vg0716355931 NA 4.79E-10 mr1578 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
vg0716355931 NA 1.07E-08 mr1648 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
vg0716355931 NA 1.31E-13 mr1871 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
vg0716355931 NA 6.74E-07 mr1696_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
vg0716355931 6.15E-07 3.60E-15 mr1705_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
vg0716355931 NA 2.75E-09 mr1705_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
vg0716355931 NA 2.65E-08 mr1819_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
vg0716355931 NA 2.71E-10 mr1993_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