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Detailed information for vg0506871793:

Variant ID: vg0506871793 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 6871793
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TATATAGTGCATATTATTTATTTATTTAGAATTTTTTATGGGGAAGGGGGATAGTTACAAAGTATGTACGTGCATGCGTACATATATGGGAGCAATCGAC[G/A]
TAGATGTTCTAATGATAAATTAAATCTATTTGTTATTTTTAGATCTAACGGTTAAAAATATGGTGTCCACTACATTAAGTGAAAATTAATAGCTAGATAT

Reverse complement sequence

ATATCTAGCTATTAATTTTCACTTAATGTAGTGGACACCATATTTTTAACCGTTAGATCTAAAAATAACAAATAGATTTAATTTATCATTAGAACATCTA[C/T]
GTCGATTGCTCCCATATATGTACGCATGCACGTACATACTTTGTAACTATCCCCCTTCCCCATAAAAAATTCTAAATAAATAAATAATATGCACTATATA

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 89.30% 10.70% 0.02% 0.00% NA
All Indica  2759 82.10% 17.90% 0.04% 0.00% NA
All Japonica  1512 99.50% 0.50% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 94.60% 5.20% 0.17% 0.00% NA
Indica II  465 70.80% 29.20% 0.00% 0.00% NA
Indica III  913 74.50% 25.50% 0.00% 0.00% NA
Indica Intermediate  786 88.20% 11.80% 0.00% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 99.00% 1.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 92.20% 7.80% 0.00% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0506871793 G -> A LOC_Os05g12020.1 upstream_gene_variant ; 2034.0bp to feature; MODIFIER silent_mutation Average:35.132; most accessible tissue: Minghui63 panicle, score: 56.842 N N N N
vg0506871793 G -> A LOC_Os05g12010.1 downstream_gene_variant ; 3552.0bp to feature; MODIFIER silent_mutation Average:35.132; most accessible tissue: Minghui63 panicle, score: 56.842 N N N N
vg0506871793 G -> A LOC_Os05g12010-LOC_Os05g12020 intergenic_region ; MODIFIER silent_mutation Average:35.132; most accessible tissue: Minghui63 panicle, score: 56.842 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0506871793 2.72E-70 1.58E-118 mr1039 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
vg0506871793 1.38E-54 3.55E-87 mr1039 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
vg0506871793 2.91E-27 1.45E-43 mr1632 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
vg0506871793 5.91E-23 6.60E-31 mr1632 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
vg0506871793 2.92E-85 2.03E-127 mr1039_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
vg0506871793 9.89E-62 5.65E-91 mr1039_2 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
vg0506871793 1.15E-11 1.07E-18 mr1514_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
vg0506871793 3.40E-10 1.59E-10 mr1514_2 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
vg0506871793 4.83E-45 1.44E-67 mr1632_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
vg0506871793 6.38E-35 3.72E-49 mr1632_2 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
vg0506871793 4.22E-09 NA mr1873_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
vg0506871793 8.14E-08 1.26E-09 mr1873_2 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