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Detailed information for vg0825998133:

Variant ID: vg0825998133 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 25998133
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGACGCACGGCATGGTGGCCTCCGCCGTGGAGCCGAGGAGCTCCACCCTGAACACCGGCGAGCGCGCGGCGAGCACGGCCCGGTGCGCGTGGAACGTCTC[A/G]
CCGCCGACGGAGAAGGACACGTCCGAGCCGTCGGCGCTGCCCACCATGGCGCCGAGCTGGCCGCCCAGGTTAGAGGGCGGCACGGCTATGGCACCACCGT

Reverse complement sequence

ACGGTGGTGCCATAGCCGTGCCGCCCTCTAACCTGGGCGGCCAGCTCGGCGCCATGGTGGGCAGCGCCGACGGCTCGGACGTGTCCTTCTCCGTCGGCGG[T/C]
GAGACGTTCCACGCGCACCGGGCCGTGCTCGCCGCGCGCTCGCCGGTGTTCAGGGTGGAGCTCCTCGGCTCCACGGCGGAGGCCACCATGCCGTGCGTCA

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 64.70% 35.10% 0.13% 0.00% NA
All Indica  2759 98.70% 1.20% 0.14% 0.00% NA
All Japonica  1512 3.00% 97.00% 0.00% 0.00% NA
Aus  269 81.00% 19.00% 0.00% 0.00% NA
Indica I  595 99.50% 0.30% 0.17% 0.00% NA
Indica II  465 98.50% 1.30% 0.22% 0.00% NA
Indica III  913 99.60% 0.40% 0.00% 0.00% NA
Indica Intermediate  786 97.20% 2.50% 0.25% 0.00% NA
Temperate Japonica  767 2.50% 97.50% 0.00% 0.00% NA
Tropical Japonica  504 2.20% 97.80% 0.00% 0.00% NA
Japonica Intermediate  241 6.60% 93.40% 0.00% 0.00% NA
VI/Aromatic  96 21.90% 78.10% 0.00% 0.00% NA
Intermediate  90 56.70% 41.10% 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
vg0825998133 A -> G LOC_Os08g41150.1 synonymous_variant ; p.Gly189Gly; LOW synonymous_codon Average:71.124; most accessible tissue: Zhenshan97 panicle, score: 83.904 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0825998133 NA 1.72E-21 mr1021 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
vg0825998133 NA 2.34E-26 mr1024 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
vg0825998133 NA 5.45E-15 mr1228 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
vg0825998133 NA 5.07E-16 mr1323 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
vg0825998133 NA 2.80E-20 mr1477 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
vg0825998133 NA 2.12E-37 mr1601 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
vg0825998133 NA 1.45E-06 mr1781 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
vg0825998133 NA 7.07E-38 mr1689_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