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Detailed information for vg0427886354:

Variant ID: vg0427886354 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 27886354
Reference Allele: AAlternative Allele: C
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.86, A: 0.15, others allele: 0.00, population size: 272. )

Flanking Sequence (100 bp) in Reference Genome:


TATGGAGGATATATAATGCATGAACATTATCTTTGTTTGAAGGCATCATGGTTGACATGCCATGATCGAGCAGCACAGCATGGAAATATATAGGTACCTT[A/C]
GCTAATAGCGAGCGTAGAAATGTTTTGCTATCTGCAGACTGAGCATTGCGCAGCCAAACAGATGCATTGCTTGCATAGCTTTTGCCTGGCAGCCTGCAGA

Reverse complement sequence

TCTGCAGGCTGCCAGGCAAAAGCTATGCAAGCAATGCATCTGTTTGGCTGCGCAATGCTCAGTCTGCAGATAGCAAAACATTTCTACGCTCGCTATTAGC[T/G]
AAGGTACCTATATATTTCCATGCTGTGCTGCTCGATCATGGCATGTCAACCATGATGCCTTCAAACAAAGATAATGTTCATGCATTATATATCCTCCATA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 50.70% 48.70% 0.15% 0.44% NA
All Indica  2759 79.80% 19.40% 0.18% 0.65% NA
All Japonica  1512 0.50% 99.40% 0.00% 0.13% NA
Aus  269 59.10% 40.90% 0.00% 0.00% NA
Indica I  595 80.00% 19.00% 0.00% 1.01% NA
Indica II  465 91.60% 8.00% 0.00% 0.43% NA
Indica III  913 75.50% 24.00% 0.11% 0.44% NA
Indica Intermediate  786 77.70% 21.00% 0.51% 0.76% NA
Temperate Japonica  767 0.30% 99.60% 0.00% 0.13% NA
Tropical Japonica  504 0.60% 99.40% 0.00% 0.00% NA
Japonica Intermediate  241 0.80% 98.80% 0.00% 0.41% NA
VI/Aromatic  96 1.00% 99.00% 0.00% 0.00% NA
Intermediate  90 30.00% 66.70% 2.22% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0427886354 A -> C LOC_Os04g47040.1 synonymous_variant ; p.Ala162Ala; LOW synonymous_codon Average:52.566; most accessible tissue: Zhenshan97 young leaf, score: 73.147 N N N N
vg0427886354 A -> DEL LOC_Os04g47040.1 N frameshift_variant Average:52.566; most accessible tissue: Zhenshan97 young leaf, score: 73.147 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0427886354 9.43E-08 8.96E-41 mr1873 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
vg0427886354 1.04E-07 1.08E-08 mr1873 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
vg0427886354 NA 2.77E-06 mr1881 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
vg0427886354 NA 3.58E-16 mr1579_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
vg0427886354 5.48E-07 1.82E-38 mr1873_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
vg0427886354 1.24E-06 8.86E-09 mr1873_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