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Detailed information for vg0803976100:

Variant ID: vg0803976100 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 3976100
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.70, G: 0.30, others allele: 0.00, population size: 105. )

Flanking Sequence (100 bp) in Reference Genome:


TTATTTTATCCTTAGCTAGGGCATCAACTATGTATATGACAAAATGATCCATATAGATGGGACACATATAAATGAACTTTAACTATAGCAATCCCACAAT[A/G]
TATATAGACACAAGGTATCATTAGAAAAAGAGAGAGGAGTAGAGATAGATAATATTATTTATTCCGCCATATGGGTAATCTATTTGCATATGGGTACCTT

Reverse complement sequence

AAGGTACCCATATGCAAATAGATTACCCATATGGCGGAATAAATAATATTATCTATCTCTACTCCTCTCTCTTTTTCTAATGATACCTTGTGTCTATATA[T/C]
ATTGTGGGATTGCTATAGTTAAAGTTCATTTATATGTGTCCCATCTATATGGATCATTTTGTCATATACATAGTTGATGCCCTAGCTAAGGATAAAATAA

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 67.10% 32.60% 0.25% 0.00% NA
All Indica  2759 79.80% 20.00% 0.18% 0.00% NA
All Japonica  1512 41.30% 58.40% 0.26% 0.00% NA
Aus  269 81.40% 18.60% 0.00% 0.00% NA
Indica I  595 91.30% 8.70% 0.00% 0.00% NA
Indica II  465 28.80% 71.00% 0.22% 0.00% NA
Indica III  913 98.50% 1.50% 0.00% 0.00% NA
Indica Intermediate  786 79.50% 20.00% 0.51% 0.00% NA
Temperate Japonica  767 62.80% 37.00% 0.13% 0.00% NA
Tropical Japonica  504 18.30% 81.50% 0.20% 0.00% NA
Japonica Intermediate  241 21.20% 78.00% 0.83% 0.00% NA
VI/Aromatic  96 79.20% 20.80% 0.00% 0.00% NA
Intermediate  90 57.80% 38.90% 3.33% 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
vg0803976100 A -> G LOC_Os08g07100.1 intron_variant ; MODIFIER silent_mutation Average:27.577; most accessible tissue: Zhenshan97 young leaf, score: 41.875 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0803976100 NA 2.29E-06 mr1002 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
vg0803976100 NA 3.03E-07 mr1182 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
vg0803976100 NA 2.07E-08 mr1565 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
vg0803976100 NA 2.34E-07 mr1650 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
vg0803976100 NA 6.70E-08 mr1002_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
vg0803976100 NA 8.79E-09 mr1406_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