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Detailed information for vg0215951295:

Variant ID: vg0215951295 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 15951295
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 336. )

Flanking Sequence (100 bp) in Reference Genome:


GTTATGGACGTGCTGAACTCAGTTGTAGTGCATGCGGATCATGGAAATCTACTAGAACCTCTTGCTGTCCCGCAGACAGCACACCGGGTTTCTCTGTATG[C/T]
GGATGATGTGGTCATGTTCTTGCGTCCTACAAGCGGGGACCTATCTCTTATCAAGCAGATTTTGGAGGTTTTTGGTCAAATTTCTGGACTAAGAACCAAT

Reverse complement sequence

ATTGGTTCTTAGTCCAGAAATTTGACCAAAAACCTCCAAAATCTGCTTGATAAGAGATAGGTCCCCGCTTGTAGGACGCAAGAACATGACCACATCATCC[G/A]
CATACAGAGAAACCCGGTGTGCTGTCTGCGGGACAGCAAGAGGTTCTAGTAGATTTCCATGATCCGCATGCACTACAACTGAGTTCAGCACGTCCATAAC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 92.90% 6.70% 0.44% 0.00% NA
All Indica  2759 97.60% 2.40% 0.04% 0.00% NA
All Japonica  1512 83.70% 15.10% 1.26% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 92.00% 7.70% 0.22% 0.00% NA
Indica III  913 97.90% 2.10% 0.00% 0.00% NA
Indica Intermediate  786 98.70% 1.30% 0.00% 0.00% NA
Temperate Japonica  767 93.20% 5.70% 1.04% 0.00% NA
Tropical Japonica  504 85.70% 13.90% 0.40% 0.00% NA
Japonica Intermediate  241 49.00% 47.30% 3.73% 0.00% NA
VI/Aromatic  96 82.30% 17.70% 0.00% 0.00% NA
Intermediate  90 93.30% 5.60% 1.11% 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
vg0215951295 C -> T LOC_Os02g27120.1 missense_variant ; p.Ala157Val; MODERATE nonsynonymous_codon ; A157V Average:64.955; most accessible tissue: Minghui63 flower, score: 76.811 unknown unknown DELETERIOUS 0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0215951295 NA 2.21E-06 mr1044 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
vg0215951295 4.82E-08 NA mr1679 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
vg0215951295 NA 3.44E-10 mr1691 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
vg0215951295 NA 3.31E-06 mr1691 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
vg0215951295 NA 6.44E-11 mr1693 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
vg0215951295 NA 1.53E-06 mr1693 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
vg0215951295 1.04E-07 NA mr1679_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
vg0215951295 NA 1.56E-07 mr1679_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
vg0215951295 NA 1.85E-12 mr1691_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
vg0215951295 NA 6.33E-06 mr1691_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