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Detailed information for vg0808034898:

Variant ID: vg0808034898 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 8034898
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.03, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:


GCAACGCAGCTACACCACTCGTCCAAGCCATGTTCTTCAATAACAATGGCCTGAGTTCATTTGATGCTGCCGAGATCTTCGACAAGCTAAGAATTGCTCC[G/A]
GATACATATTTTAATAATATCAAGGAAGCTGGAAGAATGGGAGCAGGCCTGGCATTGGCGATGACCAAGTCCTTGTACCCGAAGATTGATATTGACGCCA

Reverse complement sequence

TGGCGTCAATATCAATCTTCGGGTACAAGGACTTGGTCATCGCCAATGCCAGGCCTGCTCCCATTCTTCCAGCTTCCTTGATATTATTAAAATATGTATC[C/T]
GGAGCAATTCTTAGCTTGTCGAAGATCTCGGCAGCATCAAATGAACTCAGGCCATTGTTATTGAAGAACATGGCTTGGACGAGTGGTGTAGCTGCGTTGC

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 57.20% 40.50% 0.17% 2.09% NA
All Indica  2759 82.60% 17.20% 0.18% 0.00% NA
All Japonica  1512 11.10% 82.30% 0.13% 6.48% NA
Aus  269 48.00% 52.00% 0.00% 0.00% NA
Indica I  595 92.60% 7.40% 0.00% 0.00% NA
Indica II  465 53.80% 45.40% 0.86% 0.00% NA
Indica III  913 88.10% 11.90% 0.00% 0.00% NA
Indica Intermediate  786 85.80% 14.10% 0.13% 0.00% NA
Temperate Japonica  767 3.00% 94.00% 0.00% 3.00% NA
Tropical Japonica  504 21.40% 75.80% 0.00% 2.78% NA
Japonica Intermediate  241 15.40% 58.50% 0.83% 25.31% NA
VI/Aromatic  96 77.10% 22.90% 0.00% 0.00% NA
Intermediate  90 61.10% 36.70% 1.11% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0808034898 G -> A LOC_Os08g13500.1 synonymous_variant ; p.Pro638Pro; LOW synonymous_codon Average:43.54; most accessible tissue: Minghui63 flag leaf, score: 63.086 N N N N
vg0808034898 G -> DEL LOC_Os08g13500.1 N frameshift_variant Average:43.54; most accessible tissue: Minghui63 flag leaf, score: 63.086 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0808034898 5.29E-06 NA mr1480_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
vg0808034898 NA 6.28E-06 mr1863_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
vg0808034898 5.85E-06 5.65E-21 mr1968_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
vg0808034898 4.81E-06 8.73E-08 mr1968_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