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Detailed information for vg0615169965:

Variant ID: vg0615169965 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 15169965
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.96, G: 0.04, others allele: 0.00, population size: 53. )

Flanking Sequence (100 bp) in Reference Genome:


AGGCTAGTACCATCCCCGGTCAATTAAGGACCGAGCCATGAATTTAAGCATGAAACGACCCCCGTACAACCGCACTTCTCGTATGGGTATAGACCTAGCG[A/G]
AATAGATAGCTGAGCGGAGGCAGTATCCATGCATAGTGGTTTCTTGATGTGTGAGGTAGGGGCTCTATGGTGGGGCAGCCATTGGTAGAACCGCGAGGCA

Reverse complement sequence

TGCCTCGCGGTTCTACCAATGGCTGCCCCACCATAGAGCCCCTACCTCACACATCAAGAAACCACTATGCATGGATACTGCCTCCGCTCAGCTATCTATT[T/C]
CGCTAGGTCTATACCCATACGAGAAGTGCGGTTGTACGGGGGTCGTTTCATGCTTAAATTCATGGCTCGGTCCTTAATTGACCGGGGATGGTACTAGCCT

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 32.60% 4.30% 8.13% 54.93% NA
All Indica  2759 4.30% 0.30% 13.37% 82.02% NA
All Japonica  1512 91.30% 0.10% 0.00% 8.66% NA
Aus  269 2.60% 68.00% 4.09% 25.28% NA
Indica I  595 5.00% 0.00% 4.71% 90.25% NA
Indica II  465 2.20% 0.20% 8.17% 89.46% NA
Indica III  913 2.50% 0.00% 23.00% 74.48% NA
Indica Intermediate  786 7.00% 1.00% 11.83% 80.15% NA
Temperate Japonica  767 96.70% 0.00% 0.00% 3.26% NA
Tropical Japonica  504 82.30% 0.20% 0.00% 17.46% NA
Japonica Intermediate  241 92.50% 0.00% 0.00% 7.47% NA
VI/Aromatic  96 1.00% 4.20% 0.00% 94.79% NA
Intermediate  90 38.90% 8.90% 4.44% 47.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0615169965 A -> G LOC_Os06g25910-LOC_Os06g25920 intergenic_region ; MODIFIER silent_mutation Average:13.425; most accessible tissue: Callus, score: 26.739 N N N N
vg0615169965 A -> DEL N N silent_mutation Average:13.425; most accessible tissue: Callus, score: 26.739 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0615169965 7.64E-07 8.60E-09 mr1020 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
vg0615169965 1.10E-10 1.10E-10 mr1032 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
vg0615169965 1.27E-06 4.02E-12 mr1033 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
vg0615169965 1.32E-08 1.32E-08 mr1165 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
vg0615169965 NA 2.75E-14 mr1361 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
vg0615169965 1.33E-11 1.33E-11 mr1478 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
vg0615169965 1.09E-08 1.09E-08 mr1536 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
vg0615169965 NA 4.13E-08 mr1806 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
vg0615169965 1.07E-09 2.19E-12 mr1971 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
vg0615169965 NA 2.17E-08 mr1165_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