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Detailed information for vg0816275999:

Variant ID: vg0816275999 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 16275999
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 89. )

Flanking Sequence (100 bp) in Reference Genome:


CGCGGGTATAAAACTAAATCCGGAAAAGTGTGGTTTTGGTGTTCACGCGGGCAAGTTGCTGGGTTTTCTTATTTCCTAAAGGGGTATCGAGGCGAACCCC[A/G]
AGAAAATCGATGCCATTCAGCAAATGAAGCCCCCATCGAGCGTACTCGAAGTACAAAAGGTCGCAGGCCGAATTGCGGCACTCAGTCGATTCCTCTCAAA

Reverse complement sequence

TTTGAGAGGAATCGACTGAGTGCCGCAATTCGGCCTGCGACCTTTTGTACTTCGAGTACGCTCGATGGGGGCTTCATTTGCTGAATGGCATCGATTTTCT[T/C]
GGGGTTCGCCTCGATACCCCTTTAGGAAATAAGAAAACCCAGCAACTTGCCCGCGTGAACACCAAAACCACACTTTTCCGGATTTAGTTTTATACCCGCG

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 43.70% 40.10% 10.20% 5.99% NA
All Indica  2759 67.30% 20.80% 11.27% 0.58% NA
All Japonica  1512 8.10% 74.70% 1.32% 15.87% NA
Aus  269 23.40% 16.00% 52.79% 7.81% NA
Indica I  595 40.20% 43.90% 15.13% 0.84% NA
Indica II  465 67.30% 21.90% 10.54% 0.22% NA
Indica III  913 88.40% 3.40% 7.78% 0.44% NA
Indica Intermediate  786 63.40% 23.00% 12.85% 0.76% NA
Temperate Japonica  767 0.50% 98.60% 0.00% 0.91% NA
Tropical Japonica  504 21.40% 37.90% 2.98% 37.70% NA
Japonica Intermediate  241 4.10% 75.90% 2.07% 17.84% NA
VI/Aromatic  96 2.10% 95.80% 1.04% 1.04% NA
Intermediate  90 22.20% 63.30% 8.89% 5.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0816275999 A -> G LOC_Os08g26770.1 missense_variant ; p.Lys216Glu; MODERATE nonsynonymous_codon ; K216E Average:16.753; most accessible tissue: Callus, score: 53.972 benign -0.278 TOLERATED 1.00
vg0816275999 A -> DEL LOC_Os08g26770.1 N frameshift_variant Average:16.753; most accessible tissue: Callus, score: 53.972 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0816275999 NA 3.96E-13 Grain_thickness Jap_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0816275999 NA 1.44E-06 mr1082 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
vg0816275999 NA 3.51E-06 mr1083 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
vg0816275999 NA 5.59E-06 mr1124 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
vg0816275999 NA 2.12E-24 mr1217 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
vg0816275999 NA 2.61E-22 mr1300 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
vg0816275999 NA 2.23E-14 mr1376 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
vg0816275999 NA 2.58E-06 mr1424 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
vg0816275999 NA 2.23E-14 mr1431 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
vg0816275999 NA 7.21E-06 mr1681 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
vg0816275999 NA 4.19E-22 mr1845 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
vg0816275999 NA 6.00E-06 mr1884 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
vg0816275999 NA 6.73E-07 mr1077_2 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
vg0816275999 NA 6.42E-08 mr1526_2 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
vg0816275999 NA 2.39E-07 mr1952_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