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Detailed information for vg0816083415:

Variant ID: vg0816083415 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 16083415
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:


ACTCCTTATGGAAAAAGCGAAAGGAAATTCCATCTTCTATTTCTTTTAAAGTGCACAGAAATTGCAAAGTAAGCAAACGAGAACCAGGCTCATCTACCAC[A/G]
GCAAATCTCTGCCAACCAACAGCTTTCCAAATAGCACAAAATTCAACATCCATACCTATCTTTCTCAGCAGCTCCGGAGAGTATTCTCGCGTGTGAGCAT

Reverse complement sequence

ATGCTCACACGCGAGAATACTCTCCGGAGCTGCTGAGAAAGATAGGTATGGATGTTGAATTTTGTGCTATTTGGAAAGCTGTTGGTTGGCAGAGATTTGC[T/C]
GTGGTAGATGAGCCTGGTTCTCGTTTGCTTACTTTGCAATTTCTGTGCACTTTAAAAGAAATAGAAGATGGAATTTCCTTTCGCTTTTTCCATAAGGAGT

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 87.40% 0.60% 0.72% 11.30% NA
All Indica  2759 85.00% 0.70% 0.62% 13.70% NA
All Japonica  1512 89.70% 0.00% 0.86% 9.39% NA
Aus  269 94.10% 2.60% 1.49% 1.86% NA
Indica I  595 91.60% 0.20% 0.34% 7.90% NA
Indica II  465 77.20% 0.90% 0.86% 21.08% NA
Indica III  913 85.70% 0.80% 0.33% 13.25% NA
Indica Intermediate  786 83.80% 0.90% 1.02% 14.25% NA
Temperate Japonica  767 98.20% 0.00% 0.13% 1.69% NA
Tropical Japonica  504 83.50% 0.00% 1.79% 14.68% NA
Japonica Intermediate  241 75.90% 0.00% 1.24% 22.82% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 90.00% 0.00% 0.00% 10.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0816083415 A -> G LOC_Os08g26390.1 synonymous_variant ; p.Ala99Ala; LOW synonymous_codon Average:12.356; most accessible tissue: Minghui63 panicle, score: 20.733 N N N N
vg0816083415 A -> G LOC_Os08g26390.1 synonymous_variant ; p.Ala99Ala; LOW nonsynonymous_codon ; A99V Average:12.356; most accessible tissue: Minghui63 panicle, score: 20.733 unknown unknown TOLERATED 0.21
vg0816083415 A -> DEL LOC_Os08g26390.1 N frameshift_variant Average:12.356; most accessible tissue: Minghui63 panicle, score: 20.733 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0816083415 1.12E-06 1.12E-06 mr1184 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
vg0816083415 NA 4.41E-06 mr1236 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
vg0816083415 NA 3.76E-06 mr1236 Ind_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
vg0816083415 NA 8.51E-06 mr1352 Ind_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
vg0816083415 NA 1.87E-06 mr1654 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