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Detailed information for vg0813557256:

Variant ID: vg0813557256 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 13557256
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.58, A: 0.42, others allele: 0.00, population size: 86. )

Flanking Sequence (100 bp) in Reference Genome:


GTTCAATTTTCGTGTCCGATGGTTTGTTCAATTTGCCGAAAGTATGGGAATCAAACTGTTAAATTCTTCACCATATTATGCACAAGCTAATGGGCAAGCC[A/G]
AGGCATCTAACAAAAGCTTGATCAAGTTGATTAAGAGGAAGATTTCTGATTATCCTCGGCAATGGCATGCTCGGTTGCCCGAAGCATTGTGGTCTTATCG

Reverse complement sequence

CGATAAGACCACAATGCTTCGGGCAACCGAGCATGCCATTGCCGAGGATAATCAGAAATCTTCCTCTTAATCAACTTGATCAAGCTTTTGTTAGATGCCT[T/C]
GGCTTGCCCATTAGCTTGTGCATAATATGGTGAAGAATTTAACAGTTTGATTCCCATACTTTCGGCAAATTGAACAAACCATCGGACACGAAAATTGAAC

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 26.30% 21.10% 2.88% 49.72% NA
All Indica  2759 15.80% 4.20% 4.49% 75.50% NA
All Japonica  1512 37.80% 56.50% 0.07% 5.56% NA
Aus  269 39.00% 1.90% 2.97% 56.13% NA
Indica I  595 2.50% 2.70% 4.03% 90.76% NA
Indica II  465 12.30% 7.30% 4.95% 75.48% NA
Indica III  913 23.10% 2.10% 4.49% 70.32% NA
Indica Intermediate  786 19.50% 6.00% 4.58% 69.97% NA
Temperate Japonica  767 6.10% 85.40% 0.13% 8.34% NA
Tropical Japonica  504 74.20% 24.40% 0.00% 1.39% NA
Japonica Intermediate  241 62.70% 32.00% 0.00% 5.39% NA
VI/Aromatic  96 92.70% 2.10% 1.04% 4.17% NA
Intermediate  90 43.30% 23.30% 2.22% 31.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0813557256 A -> G LOC_Os08g22500.1 missense_variant ; p.Lys442Glu; MODERATE nonsynonymous_codon ; K442E Average:16.46; most accessible tissue: Callus, score: 56.714 benign -0.281 TOLERATED 1.00
vg0813557256 A -> DEL LOC_Os08g22500.1 N frameshift_variant Average:16.46; most accessible tissue: Callus, score: 56.714 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0813557256 NA 2.30E-14 Plant_height 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
vg0813557256 NA 2.47E-06 mr1063 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
vg0813557256 NA 2.41E-08 mr1180 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
vg0813557256 NA 2.08E-11 mr1183 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
vg0813557256 NA 1.24E-06 mr1238 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
vg0813557256 NA 4.03E-06 mr1309 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
vg0813557256 NA 3.88E-06 mr1330 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
vg0813557256 NA 8.50E-12 mr1503 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
vg0813557256 NA 4.50E-07 mr1617 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
vg0813557256 NA 3.05E-06 mr1794 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
vg0813557256 NA 1.34E-06 mr1841 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
vg0813557256 6.64E-06 6.64E-06 mr1900 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
vg0813557256 NA 1.03E-10 mr1180_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
vg0813557256 NA 1.06E-10 mr1183_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
vg0813557256 NA 5.50E-06 mr1194_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
vg0813557256 NA 4.88E-07 mr1521_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
vg0813557256 NA 4.22E-13 mr1794_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