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Detailed information for vg0206233846:

Variant ID: vg0206233846 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 6233846
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGGATTCTCGGTGGAGAATCCGAACTTTGGAAAACATCTTTGCGTCTCTACTTTGGTTTGCTTGTATTTTGAATTCTTGTCTTGATTTGTGCTTTTCTTT[A/G]
ATCTACTCGGTTGTGCATGTATTTGGGTGCAGGTGCTTCGTGGCTTTACGAAAGAACAACATATGACACACTGCACATTAGTTGCTTTGATCTAGAACTC

Reverse complement sequence

GAGTTCTAGATCAAAGCAACTAATGTGCAGTGTGTCATATGTTGTTCTTTCGTAAAGCCACGAAGCACCTGCACCCAAATACATGCACAACCGAGTAGAT[T/C]
AAAGAAAAGCACAAATCAAGACAAGAATTCAAAATACAAGCAAACCAAAGTAGAGACGCAAAGATGTTTTCCAAAGTTCGGATTCTCCACCGAGAATCCC

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 55.50% 44.40% 0.15% 0.00% NA
All Indica  2759 38.50% 61.30% 0.18% 0.00% NA
All Japonica  1512 96.90% 3.10% 0.00% 0.00% NA
Aus  269 2.20% 97.40% 0.37% 0.00% NA
Indica I  595 52.40% 47.60% 0.00% 0.00% NA
Indica II  465 50.80% 49.20% 0.00% 0.00% NA
Indica III  913 28.00% 71.70% 0.22% 0.00% NA
Indica Intermediate  786 33.00% 66.70% 0.38% 0.00% NA
Temperate Japonica  767 98.20% 1.80% 0.00% 0.00% NA
Tropical Japonica  504 95.80% 4.20% 0.00% 0.00% NA
Japonica Intermediate  241 95.00% 5.00% 0.00% 0.00% NA
VI/Aromatic  96 40.60% 59.40% 0.00% 0.00% NA
Intermediate  90 54.40% 44.40% 1.11% 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
vg0206233846 A -> G LOC_Os02g12010.1 upstream_gene_variant ; 1861.0bp to feature; MODIFIER silent_mutation Average:39.077; most accessible tissue: Callus, score: 57.026 N N N N
vg0206233846 A -> G LOC_Os02g12020.1 downstream_gene_variant ; 2860.0bp to feature; MODIFIER silent_mutation Average:39.077; most accessible tissue: Callus, score: 57.026 N N N N
vg0206233846 A -> G LOC_Os02g12010-LOC_Os02g12020 intergenic_region ; MODIFIER silent_mutation Average:39.077; most accessible tissue: Callus, score: 57.026 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0206233846 5.12E-08 5.64E-19 mr1170 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
vg0206233846 1.17E-07 1.33E-12 mr1170 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
vg0206233846 NA 2.15E-06 mr1740 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
vg0206233846 2.52E-07 8.60E-18 mr1170_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
vg0206233846 4.08E-06 1.10E-10 mr1170_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
vg0206233846 NA 6.91E-07 mr1691_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
vg0206233846 NA 4.40E-07 mr1743_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
vg0206233846 NA 3.09E-07 mr1749_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