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Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0318691018:

Variant ID: vg0318691018 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 18691018
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 58. )

Flanking Sequence (100 bp) in Reference Genome:


GGGACATTTACAGGGGGTACATAATGTTATGGAGGTTCATGGGCCCCTGATGGGCCGTCGGGCGACCGCCGGCCCTATAGCCCCTAGGCTTGATGGGCCG[G/A]
AAAGGCTTCTTCGGCCCTCGCGGGGGCGAACTTGCCATGGCGAAATCGTCTTCCTTCGGCAGATACTCTTCGCCTTGCACCCTTCGCCTGGGACGCCTCT

Reverse complement sequence

AGAGGCGTCCCAGGCGAAGGGTGCAAGGCGAAGAGTATCTGCCGAAGGAAGACGATTTCGCCATGGCAAGTTCGCCCCCGCGAGGGCCGAAGAAGCCTTT[C/T]
CGGCCCATCAAGCCTAGGGGCTATAGGGCCGGCGGTCGCCCGACGGCCCATCAGGGGCCCATGAACCTCCATAACATTATGTACCCCCTGTAAATGTCCC

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 94.50% 4.90% 0.02% 0.59% NA
All Indica  2759 99.10% 0.80% 0.00% 0.11% NA
All Japonica  1512 98.50% 0.10% 0.00% 1.46% NA
Aus  269 29.70% 69.90% 0.37% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 98.90% 1.10% 0.00% 0.00% NA
Indica Intermediate  786 98.10% 1.50% 0.00% 0.38% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.00% 0.00% 0.20% NA
Japonica Intermediate  241 90.90% 0.40% 0.00% 8.71% NA
VI/Aromatic  96 75.00% 21.90% 0.00% 3.12% NA
Intermediate  90 98.90% 1.10% 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
vg0318691018 G -> A LOC_Os03g32630.1 upstream_gene_variant ; 1630.0bp to feature; MODIFIER silent_mutation Average:61.496; most accessible tissue: Minghui63 young leaf, score: 75.006 N N N N
vg0318691018 G -> A LOC_Os03g32636.1 upstream_gene_variant ; 37.0bp to feature; MODIFIER silent_mutation Average:61.496; most accessible tissue: Minghui63 young leaf, score: 75.006 N N N N
vg0318691018 G -> A LOC_Os03g32642.1 downstream_gene_variant ; 3515.0bp to feature; MODIFIER silent_mutation Average:61.496; most accessible tissue: Minghui63 young leaf, score: 75.006 N N N N
vg0318691018 G -> A LOC_Os03g32630-LOC_Os03g32636 intergenic_region ; MODIFIER silent_mutation Average:61.496; most accessible tissue: Minghui63 young leaf, score: 75.006 N N N N
vg0318691018 G -> DEL N N silent_mutation Average:61.496; most accessible tissue: Minghui63 young leaf, score: 75.006 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0318691018 9.89E-06 NA mr1911_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
vg0318691018 2.28E-06 NA mr1911_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