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Detailed information for vg0506869876:

Variant ID: vg0506869876 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 6869876
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGCGGCGGCATGGTGTGGCTTCTTTTACCATCCATCTCATTAAGAGTGGTCACTACGTATATGCTCAATTTAGAAAAACCTTAGAGCCTGGAAAGAAAGA[G/C]
AAAACTACCATATGGGGCATACCATATACACACTCTTCTTTTTTTCTTTTTATATTTCTTGCGTATGTATGTACATAGGAGTTGTGTATGTACATAAGGA

Reverse complement sequence

TCCTTATGTACATACACAACTCCTATGTACATACATACGCAAGAAATATAAAAAGAAAAAAAGAAGAGTGTGTATATGGTATGCCCCATATGGTAGTTTT[C/G]
TCTTTCTTTCCAGGCTCTAAGGTTTTTCTAAATTGAGCATATACGTAGTGACCACTCTTAATGAGATGGATGGTAAAAGAAGCCACACCATGCCGCCGCC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 89.30% 10.70% 0.00% 0.00% NA
All Indica  2759 82.10% 17.90% 0.00% 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% 5.40% 0.00% 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 93.30% 6.70% 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
vg0506869876 G -> C LOC_Os05g12020.1 upstream_gene_variant ; 3951.0bp to feature; MODIFIER silent_mutation Average:39.455; most accessible tissue: Zhenshan97 flower, score: 49.187 N N N N
vg0506869876 G -> C LOC_Os05g12010.1 downstream_gene_variant ; 1635.0bp to feature; MODIFIER silent_mutation Average:39.455; most accessible tissue: Zhenshan97 flower, score: 49.187 N N N N
vg0506869876 G -> C LOC_Os05g12010-LOC_Os05g12020 intergenic_region ; MODIFIER silent_mutation Average:39.455; most accessible tissue: Zhenshan97 flower, score: 49.187 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0506869876 1.30E-70 2.07E-123 mr1039 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
vg0506869876 2.68E-54 2.03E-90 mr1039 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
vg0506869876 1.99E-24 1.30E-41 mr1632 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
vg0506869876 2.19E-20 1.04E-28 mr1632 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
vg0506869876 5.18E-84 2.78E-132 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
vg0506869876 1.03E-59 1.19E-93 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
vg0506869876 6.36E-12 1.88E-19 mr1514_2 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
vg0506869876 1.73E-10 5.85E-11 mr1514_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
vg0506869876 2.91E-42 1.66E-66 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
vg0506869876 3.37E-32 2.62E-47 mr1632_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
vg0506869876 1.80E-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
vg0506869876 4.68E-08 4.35E-10 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