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Detailed information for vg0332229065:

Variant ID: vg0332229065 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 32229065
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCTCTCGCTCGGCGCCCAGATTCCAAGGCGCGTTCCCGTCGATCTTCAGCCTCCTTTGCAATCCGTTCGCGGTCTTGTTGTTCACGCTGTAGTCGTTCTC[G/A]
CTCCTGTCACTGTCGCTCTTCCTCCAGTCGGCGACGTTCAGCTTCTTGCCGTGCGCGATCTTGGTCCGCTTCTCGGGCTTGACGCTGTTCCTCCGTTTCG

Reverse complement sequence

CGAAACGGAGGAACAGCGTCAAGCCCGAGAAGCGGACCAAGATCGCGCACGGCAAGAAGCTGAACGTCGCCGACTGGAGGAAGAGCGACAGTGACAGGAG[C/T]
GAGAACGACTACAGCGTGAACAACAAGACCGCGAACGGATTGCAAAGGAGGCTGAAGATCGACGGGAACGCGCCTTGGAATCTGGGCGCCGAGCGAGAGA

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 94.80% 4.80% 0.40% 0.00% NA
All Indica  2759 91.30% 8.00% 0.69% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 98.50% 1.50% 0.00% 0.00% NA
Indica II  465 98.90% 1.10% 0.00% 0.00% NA
Indica III  913 86.20% 12.90% 0.88% 0.00% NA
Indica Intermediate  786 87.40% 11.20% 1.40% 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  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 94.40% 5.60% 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
vg0332229065 G -> A LOC_Os03g56572.1 synonymous_variant ; p.Ser119Ser; LOW synonymous_codon Average:24.833; most accessible tissue: Zhenshan97 root, score: 39.742 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0332229065 NA 3.80E-06 mr1728 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
vg0332229065 NA 4.64E-06 mr1138_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
vg0332229065 NA 5.43E-06 mr1728_2 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
vg0332229065 3.75E-06 5.19E-07 mr1860_2 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