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Detailed information for vg0806619995:

Variant ID: vg0806619995 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 6619995
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, A: 0.00, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:


GATGTTGCAGGACGTCAAGGAGGACTGTGAAATTGAAAAGGAGGTCCAGAAATTGGAGCGTATGTTAGCGGACCACAGGACACCGTTATACCCAGGTTGC[G/A]
AGTAGGGGCATAAAAAGTTGGGTAACACTATGGAATTCTTGCAATGGAAGGCAAAATGTGGTCTGAGTGACAAGGCATTTGGCGACTTATTGAAACTAGT

Reverse complement sequence

ACTAGTTTCAATAAGTCGCCAAATGCCTTGTCACTCAGACCACATTTTGCCTTCCATTGCAAGAATTCCATAGTGTTACCCAACTTTTTATGCCCCTACT[C/T]
GCAACCTGGGTATAACGGTGTCCTGTGGTCCGCTAACATACGCTCCAATTTCTGGACCTCCTTTTCAATTTCACAGTCCTCCTTGACGTCCTGCAACATC

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 90.40% 0.10% 3.96% 5.54% NA
All Indica  2759 83.80% 0.10% 6.74% 9.35% NA
All Japonica  1512 99.90% 0.00% 0.00% 0.07% NA
Aus  269 99.30% 0.40% 0.37% 0.00% NA
Indica I  595 69.10% 0.20% 5.21% 25.55% NA
Indica II  465 90.80% 0.20% 3.44% 5.59% NA
Indica III  913 86.70% 0.00% 11.28% 1.97% NA
Indica Intermediate  786 87.40% 0.10% 4.58% 7.89% NA
Temperate Japonica  767 99.90% 0.00% 0.00% 0.13% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 96.70% 0.00% 0.00% 3.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0806619995 G -> A LOC_Os08g11260.1 intron_variant ; MODIFIER silent_mutation Average:14.052; most accessible tissue: Minghui63 panicle, score: 25.313 N N N N
vg0806619995 G -> DEL N N silent_mutation Average:14.052; most accessible tissue: Minghui63 panicle, score: 25.313 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0806619995 2.76E-06 2.63E-06 mr1856 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