Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923).

Detailed information for vg0817589164:

Variant ID: vg0817589164 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 17589164
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGGAATGGATGTATCATTGGCCGAGGTTTTTGTCTTCATATAGAAATGAAGTGTCTAAATTTATTGGTATTGCAAAGGCACACGCTGAGAAGAACAATAT[G/A]
AGAAAGATAATTTGTTCAAGTGCTGACTGTAAGAATGAAATAGCCTGGGAAAATGCTTCTAAAGTGAAGGAGCACTTAGTAACTCGTGGATTTATGGACA

Reverse complement sequence

TGTCCATAAATCCACGAGTTACTAAGTGCTCCTTCACTTTAGAAGCATTTTCCCAGGCTATTTCATTCTTACAGTCAGCACTTGAACAAATTATCTTTCT[C/T]
ATATTGTTCTTCTCAGCGTGTGCCTTTGCAATACCAATAAATTTAGACACTTCATTTCTATATGAAGACAAAAACCTCGGCCAATGATACATCCATTCCC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 94.40% 5.40% 0.15% 0.00% NA
All Indica  2759 97.30% 2.60% 0.14% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 33.80% 65.80% 0.37% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 97.20% 1.90% 0.86% 0.00% NA
Indica III  913 97.20% 2.80% 0.00% 0.00% NA
Indica Intermediate  786 95.50% 4.50% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 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 90.00% 7.80% 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
vg0817589164 G -> A LOC_Os08g28750.1 missense_variant ; p.Met112Ile; MODERATE nonsynonymous_codon ; M112I Average:30.498; most accessible tissue: Minghui63 flag leaf, score: 43.614 benign 0.794 DELETERIOUS 0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0817589164 NA 1.76E-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
vg0817589164 6.72E-10 8.60E-14 mr1836 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
vg0817589164 NA 5.72E-09 mr1906 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
vg0817589164 NA 2.52E-06 mr1960 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