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Detailed information for vg0905973876:

Variant ID: vg0905973876 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 5973876
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.62, A: 0.38, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:


GTCAGACCGGGCACCGGTCAGACTGAGGGTACAGTGGCGGTCAGACCAGCTACTGTACTTCGGTCAGACCGGCCTCGCAGAGATTTTTCTAAAATTCTCA[G/A]
ACTGTTTTTGCACGTGGATATATGCCTATTAGATCTACTGGTCATGTGTCTCAGTACTGGATTCCTAAATTTTTATTATCTAACCCCAGTATTGAGGCTT

Reverse complement sequence

AAGCCTCAATACTGGGGTTAGATAATAAAAATTTAGGAATCCAGTACTGAGACACATGACCAGTAGATCTAATAGGCATATATCCACGTGCAAAAACAGT[C/T]
TGAGAATTTTAGAAAAATCTCTGCGAGGCCGGTCTGACCGAAGTACAGTAGCTGGTCTGACCGCCACTGTACCCTCAGTCTGACCGGTGCCCGGTCTGAC

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 61.90% 38.10% 0.00% 0.00% NA
All Indica  2759 87.80% 12.20% 0.00% 0.00% NA
All Japonica  1512 6.50% 93.50% 0.00% 0.00% NA
Aus  269 97.40% 2.60% 0.00% 0.00% NA
Indica I  595 83.40% 16.60% 0.00% 0.00% NA
Indica II  465 94.00% 6.00% 0.00% 0.00% NA
Indica III  913 87.70% 12.30% 0.00% 0.00% NA
Indica Intermediate  786 87.70% 12.30% 0.00% 0.00% NA
Temperate Japonica  767 1.60% 98.40% 0.00% 0.00% NA
Tropical Japonica  504 2.60% 97.40% 0.00% 0.00% NA
Japonica Intermediate  241 30.30% 69.70% 0.00% 0.00% NA
VI/Aromatic  96 94.80% 5.20% 0.00% 0.00% NA
Intermediate  90 56.70% 43.30% 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
vg0905973876 G -> A LOC_Os09g10890.1 intron_variant ; MODIFIER silent_mutation Average:55.739; most accessible tissue: Minghui63 panicle, score: 77.956 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0905973876 NA 6.25E-17 mr1116 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
vg0905973876 NA 1.51E-06 mr1242 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
vg0905973876 NA 7.99E-17 mr1114_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
vg0905973876 NA 4.48E-06 mr1240_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
vg0905973876 7.07E-07 1.85E-09 mr1350_2 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