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Detailed information for vg0416883574:

Variant ID: vg0416883574 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 16883574
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, C: 0.01, others allele: 0.00, population size: 119. )

Flanking Sequence (100 bp) in Reference Genome:


AAAATGACTTGTAGACTACTATAAAAAAATGTTTTCGTAGATGCCCTCCATTTTGCTGCATAGAGGGTTTTCTAGGCCACAATTCTACATGTGGATGGGT[T/C]
AGGCTATTTAATTTTTTGAGATGATTGTTTTAACATACTCTCTATAAAAGTATAATATTTTCATAGACGGTCGGTCAAAGCCTGTTGATCTAAAAGCACA

Reverse complement sequence

TGTGCTTTTAGATCAACAGGCTTTGACCGACCGTCTATGAAAATATTATACTTTTATAGAGAGTATGTTAAAACAATCATCTCAAAAAATTAAATAGCCT[A/G]
ACCCATCCACATGTAGAATTGTGGCCTAGAAAACCCTCTATGCAGCAAAATGGAGGGCATCTACGAAAACATTTTTTTATAGTAGTCTACAAGTCATTTT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 83.40% 12.70% 1.38% 2.54% NA
All Indica  2759 89.20% 6.10% 1.63% 3.04% NA
All Japonica  1512 71.20% 26.80% 0.99% 1.06% NA
Aus  269 95.90% 0.00% 0.37% 3.72% NA
Indica I  595 88.60% 7.40% 1.34% 2.69% NA
Indica II  465 68.40% 14.20% 6.02% 11.40% NA
Indica III  913 98.80% 1.10% 0.00% 0.11% NA
Indica Intermediate  786 90.80% 6.20% 1.15% 1.78% NA
Temperate Japonica  767 92.20% 7.20% 0.65% 0.00% NA
Tropical Japonica  504 39.50% 56.70% 1.19% 2.58% NA
Japonica Intermediate  241 70.50% 26.60% 1.66% 1.24% NA
VI/Aromatic  96 76.00% 13.50% 0.00% 10.42% NA
Intermediate  90 81.10% 14.40% 4.44% 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
vg0416883574 T -> C LOC_Os04g28520.1 intron_variant ; MODIFIER silent_mutation Average:17.619; most accessible tissue: Zhenshan97 flower, score: 33.783 N N N N
vg0416883574 T -> C LOC_Os04g28520.2 intron_variant ; MODIFIER silent_mutation Average:17.619; most accessible tissue: Zhenshan97 flower, score: 33.783 N N N N
vg0416883574 T -> DEL N N silent_mutation Average:17.619; most accessible tissue: Zhenshan97 flower, score: 33.783 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0416883574 NA 1.34E-08 mr1077 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
vg0416883574 NA 9.25E-07 mr1121 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
vg0416883574 NA 4.64E-08 mr1124 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
vg0416883574 NA 6.57E-06 mr1202 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
vg0416883574 NA 8.91E-10 mr1251 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
vg0416883574 NA 9.90E-06 mr1887 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
vg0416883574 NA 1.19E-07 mr1449_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
vg0416883574 NA 5.98E-09 mr1454_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
vg0416883574 NA 4.18E-07 mr1606_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
vg0416883574 NA 1.41E-06 mr1819_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
vg0416883574 9.04E-06 NA mr1851_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
vg0416883574 NA 6.51E-06 mr1853_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
vg0416883574 NA 3.76E-06 mr1888_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
vg0416883574 NA 1.34E-08 mr1980_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