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Detailed information for vg0215987623:

Variant ID: vg0215987623 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 15987623
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 318. )

Flanking Sequence (100 bp) in Reference Genome:


ACCAATTCCAGATTTTCAGACTTATTCCTTCCAAACCAGCAGCCAATTTTGAGAGTCCCAGAAATATACCTCAAAATATGTTTTACTGCGGCCCAATGTT[C/T]
AGAAGTTGGCTTTTCCATAAATCTACTTACATATCCAACTGAATACGCAAGATCAGGCCTAGTATTCACCAAATATCGGAGACTTCCCACAATGCTTCTA

Reverse complement sequence

TAGAAGCATTGTGGGAAGTCTCCGATATTTGGTGAATACTAGGCCTGATCTTGCGTATTCAGTTGGATATGTAAGTAGATTTATGGAAAAGCCAACTTCT[G/A]
AACATTGGGCCGCAGTAAAACATATTTTGAGGTATATTTCTGGGACTCTCAAAATTGGCTGCTGGTTTGGAAGGAATAAGTCTGAAAATCTGGAATTGGT

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 96.10% 3.90% 0.00% 0.00% NA
All Indica  2759 99.10% 0.90% 0.00% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 41.60% 58.40% 0.00% 0.00% NA
Indica I  595 99.70% 0.30% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.30% 0.70% 0.00% 0.00% NA
Indica Intermediate  786 98.00% 2.00% 0.00% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 98.90% 1.10% 0.00% 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
vg0215987623 C -> T LOC_Os02g27160.1 missense_variant ; p.Glu527Lys; MODERATE nonsynonymous_codon ; E527K Average:62.377; most accessible tissue: Zhenshan97 flower, score: 82.111 benign 0.917 TOLERATED 0.08

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0215987623 NA 5.35E-07 mr1184 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
vg0215987623 NA 3.69E-07 mr1262 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
vg0215987623 6.36E-06 9.21E-43 mr1549 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
vg0215987623 1.26E-10 1.02E-52 mr1550 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
vg0215987623 8.38E-07 1.51E-43 mr1757 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
vg0215987623 NA 1.44E-06 mr1762 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
vg0215987623 NA 4.74E-32 mr1549_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
vg0215987623 2.35E-07 1.68E-51 mr1550_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
vg0215987623 NA 4.32E-28 mr1757_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