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Detailed information for vg0906782983:

Variant ID: vg0906782983 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 6782983
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.93, A: 0.07, others allele: 0.00, population size: 96. )

Flanking Sequence (100 bp) in Reference Genome:


AGTGTTAACAATGTTAGAACAAATTGTTTACACCCAAATTTGGCACCTCGGATTAAAATAGGAAAGATTGCCAAAATTTGGAAGTCTACCGATTTCCTCC[G/A]
AGTGGGCCGGTCTGACCGCCGTGTGTTGGGCGGTCAGACCGCCGGTTGAGGGCCGGTCAGACCGGCGGTGTGTGGCCGGTCTGACTAGCAGGTCCGAGTC

Reverse complement sequence

GACTCGGACCTGCTAGTCAGACCGGCCACACACCGCCGGTCTGACCGGCCCTCAACCGGCGGTCTGACCGCCCAACACACGGCGGTCAGACCGGCCCACT[C/T]
GGAGGAAATCGGTAGACTTCCAAATTTTGGCAATCTTTCCTATTTTAATCCGAGGTGCCAAATTTGGGTGTAAACAATTTGTTCTAACATTGTTAACACT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 89.80% 5.10% 5.04% 0.00% NA
All Indica  2759 98.80% 0.60% 0.58% 0.00% NA
All Japonica  1512 71.10% 14.60% 14.29% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 95.70% 1.90% 2.37% 0.00% NA
Indica III  913 99.70% 0.20% 0.11% 0.00% NA
Indica Intermediate  786 98.90% 0.60% 0.51% 0.00% NA
Temperate Japonica  767 91.80% 5.60% 2.61% 0.00% NA
Tropical Japonica  504 33.90% 31.00% 35.12% 0.00% NA
Japonica Intermediate  241 83.00% 9.10% 7.88% 0.00% NA
VI/Aromatic  96 96.90% 3.10% 0.00% 0.00% NA
Intermediate  90 91.10% 2.20% 6.67% 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
vg0906782983 G -> A LOC_Os09g12020-LOC_Os09g12050 intergenic_region ; MODIFIER silent_mutation Average:52.436; most accessible tissue: Zhenshan97 flower, score: 70.434 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0906782983 9.49E-08 2.09E-16 mr1871 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
vg0906782983 NA 1.62E-08 mr1871 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
vg0906782983 NA 1.13E-09 mr1705_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
vg0906782983 4.25E-06 2.67E-14 mr1742_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
vg0906782983 4.57E-07 6.05E-20 mr1871_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