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Detailed information for vg0622692751:

Variant ID: vg0622692751 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 22692751
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, A: 0.02, T: 0.00, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:


GCATGATAGTGGGTTAGCTGCAAAGAATGATCCGTTTAAATTCTCTTTGATTTCAAGGTTGATCTGGTCGCTGCCGTGACAATTTGCTGCATGACTCCAT[G/A]
AGGATTGAGGATGGTCGCACCGTCCTTTGATGTTGCTTTTCTCTGTACCGGGTATCGATTCCGTATAGACCATCTTGTCAATTAAAATTCGGTGGCACCA

Reverse complement sequence

TGGTGCCACCGAATTTTAATTGACAAGATGGTCTATACGGAATCGATACCCGGTACAGAGAAAAGCAACATCAAAGGACGGTGCGACCATCCTCAATCCT[C/T]
ATGGAGTCATGCAGCAAATTGTCACGGCAGCGACCAGATCAACCTTGAAATCAAAGAGAATTTAAACGGATCATTCTTTGCAGCTAACCCACTATCATGC

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 89.40% 10.60% 0.00% 0.00% NA
All Indica  2759 87.60% 12.40% 0.00% 0.00% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 43.90% 56.10% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 91.20% 8.80% 0.00% 0.00% NA
Indica III  913 74.70% 25.30% 0.00% 0.00% NA
Indica Intermediate  786 91.20% 8.80% 0.00% 0.00% NA
Temperate Japonica  767 99.60% 0.40% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 96.70% 3.30% 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
vg0622692751 G -> A LOC_Os06g38310-LOC_Os06g38320 intergenic_region ; MODIFIER silent_mutation Average:67.086; most accessible tissue: Callus, score: 82.447 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0622692751 NA 2.26E-06 mr1320 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
vg0622692751 NA 2.48E-06 mr1432 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
vg0622692751 NA 2.27E-06 mr1633 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
vg0622692751 4.51E-06 NA mr1224_2 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