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Detailed information for vg1213932089:

Variant ID: vg1213932089 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 13932089
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, G: 0.01, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:


TCTCAATAATTGTCCTTTGCTCGTTGCTGAGCCCTTCAATCAAATTGGAAAAGTATGTGATGTTTAGTCTGCTTCTTGGTTTTGGGGACTCTGCACTTCC[A/G]
GATTGATCTTGGTCATATTCAAGTTTTGTGCGCTGGAAGAAAAAAAATAGAGATTTAATTATGTCTTGTTAACAAAGAACAACATAAACTAATTAGTATA

Reverse complement sequence

TATACTAATTAGTTTATGTTGTTCTTTGTTAACAAGACATAATTAAATCTCTATTTTTTTTCTTCCAGCGCACAAAACTTGAATATGACCAAGATCAATC[T/C]
GGAAGTGCAGAGTCCCCAAAACCAAGAAGCAGACTAAACATCACATACTTTTCCAATTTGATTGAAGGGCTCAGCAACGAGCAAAGGACAATTATTGAGA

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 90.80% 9.20% 0.04% 0.00% NA
All Indica  2759 94.30% 5.70% 0.07% 0.00% NA
All Japonica  1512 99.60% 0.40% 0.00% 0.00% NA
Aus  269 22.30% 77.70% 0.00% 0.00% NA
Indica I  595 90.40% 9.40% 0.17% 0.00% NA
Indica II  465 98.30% 1.70% 0.00% 0.00% NA
Indica III  913 96.30% 3.70% 0.00% 0.00% NA
Indica Intermediate  786 92.50% 7.40% 0.13% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 98.80% 1.20% 0.00% 0.00% NA
VI/Aromatic  96 42.70% 57.30% 0.00% 0.00% NA
Intermediate  90 90.00% 10.00% 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
vg1213932089 A -> G LOC_Os12g24410.1 synonymous_variant ; p.Ser89Ser; LOW synonymous_codon Average:18.004; most accessible tissue: Zhenshan97 root, score: 27.411 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1213932089 NA 2.26E-06 mr1060 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
vg1213932089 NA 8.89E-06 mr1060 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
vg1213932089 NA 1.96E-06 mr1333 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
vg1213932089 5.89E-07 5.89E-07 mr1682 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
vg1213932089 NA 5.83E-06 mr1686 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