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Detailed information for vg0413666850:

Variant ID: vg0413666850 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 13666850
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.77, A: 0.23, others allele: 0.00, population size: 173. )

Flanking Sequence (100 bp) in Reference Genome:


TGGGTAGATGGTGAGGCTGTTGGAGCGAGTAACTAGTTTGACTAGCCAAATCAGATGGAAAGTTAGCTATGTGGGTGTTTGGAGAGTCCGATTTAGATAT[G/A]
CTGTTGAAGATGCTCTTAATCTTTGTCAATTGGGTCAATTAACATGCATGCCAGAAAGAAATTAAACCTAAGGTTTTTTTTTGTTTTATTCGTCCTAATG

Reverse complement sequence

CATTAGGACGAATAAAACAAAAAAAAACCTTAGGTTTAATTTCTTTCTGGCATGCATGTTAATTGACCCAATTGACAAAGATTAAGAGCATCTTCAACAG[C/T]
ATATCTAAATCGGACTCTCCAAACACCCACATAGCTAACTTTCCATCTGATTTGGCTAGTCAAACTAGTTACTCGCTCCAACAGCCTCACCATCTACCCA

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 68.80% 31.20% 0.02% 0.00% NA
All Indica  2759 97.00% 3.00% 0.00% 0.00% NA
All Japonica  1512 11.80% 88.20% 0.00% 0.00% NA
Aus  269 94.40% 5.60% 0.00% 0.00% NA
Indica I  595 97.50% 2.50% 0.00% 0.00% NA
Indica II  465 97.40% 2.60% 0.00% 0.00% NA
Indica III  913 97.60% 2.40% 0.00% 0.00% NA
Indica Intermediate  786 95.80% 4.20% 0.00% 0.00% NA
Temperate Japonica  767 2.00% 98.00% 0.00% 0.00% NA
Tropical Japonica  504 18.10% 81.90% 0.00% 0.00% NA
Japonica Intermediate  241 30.30% 69.70% 0.00% 0.00% NA
VI/Aromatic  96 87.50% 12.50% 0.00% 0.00% NA
Intermediate  90 62.20% 36.70% 1.11% 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
vg0413666850 G -> A LOC_Os04g23890-LOC_Os04g23910 intergenic_region ; MODIFIER silent_mutation Average:58.763; most accessible tissue: Minghui63 root, score: 72.958 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0413666850 NA 5.79E-36 mr1350 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
vg0413666850 NA 5.69E-06 mr1866 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
vg0413666850 3.10E-06 4.63E-31 mr1350_2 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
vg0413666850 3.24E-06 7.07E-11 mr1350_2 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
vg0413666850 9.54E-06 1.38E-18 mr1730_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
vg0413666850 4.36E-07 1.34E-08 mr1730_2 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
vg0413666850 NA 7.06E-16 mr1866_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
vg0413666850 NA 4.85E-06 mr1866_2 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