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Detailed information for vg0232881115:

Variant ID: vg0232881115 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 32881115
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TAAAAAAGTCAACGGCGTCAAATATTTTGGGATGCAGGGAGTACTTTTTATCAGAAAACTATAGCTTTATTTTGACAGGTTCTAGACTCTCTCATCATAT[A/G]
CACATGAAATACTTATATCGGTGTAAGTTTACCCCACATATTGTGCACCCGTAGTAGATAAAATTATAATTTTGTAAAAAATCAATTGTTATTGTTGTTG

Reverse complement sequence

CAACAACAATAACAATTGATTTTTTACAAAATTATAATTTTATCTACTACGGGTGCACAATATGTGGGGTAAACTTACACCGATATAAGTATTTCATGTG[T/C]
ATATGATGAGAGAGTCTAGAACCTGTCAAAATAAAGCTATAGTTTTCTGATAAAAAGTACTCCCTGCATCCCAAAATATTTGACGCCGTTGACTTTTTTA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 97.70% 1.30% 1.08% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 92.90% 3.90% 3.24% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 86.70% 7.20% 6.13% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 97.50% 1.70% 0.83% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 97.80% 0.00% 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
vg0232881115 A -> G LOC_Os02g53710-LOC_Os02g53720 intergenic_region ; MODIFIER silent_mutation Average:46.405; most accessible tissue: Minghui63 panicle, score: 71.773 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0232881115 NA 6.65E-06 mr1210 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
vg0232881115 2.27E-06 NA mr1682 Jap_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