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Detailed information for vg0502469018:

Variant ID: vg0502469018 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 2469018
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTAATTAATATGCAGGGTTTACAATTTCGTTTTCTGAAAATTTTGGTGATTTAGGTAGGACCAAAATTTTTTGAAATTTTGAAAGATTTTGAATGAATTT[A/G]
AATAAACTTTGACCAAATTTCACAAAAAATTGAGGAAACCCAAAAATTTCGGTCGGTATATTAATTGATTTGCCGGTGGGGTCCAAAATTATTTCCGAAA

Reverse complement sequence

TTTCGGAAATAATTTTGGACCCCACCGGCAAATCAATTAATATACCGACCGAAATTTTTGGGTTTCCTCAATTTTTTGTGAAATTTGGTCAAAGTTTATT[T/C]
AAATTCATTCAAAATCTTTCAAAATTTCAAAAAATTTTGGTCCTACCTAAATCACCAAAATTTTCAGAAAACGAAATTGTAAACCCTGCATATTAATTAG

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 65.30% 34.60% 0.13% 0.00% NA
All Indica  2759 93.70% 6.30% 0.07% 0.00% NA
All Japonica  1512 11.60% 88.30% 0.07% 0.00% NA
Aus  269 98.50% 0.70% 0.74% 0.00% NA
Indica I  595 90.80% 8.90% 0.34% 0.00% NA
Indica II  465 96.60% 3.40% 0.00% 0.00% NA
Indica III  913 93.80% 6.20% 0.00% 0.00% NA
Indica Intermediate  786 94.00% 6.00% 0.00% 0.00% NA
Temperate Japonica  767 3.70% 96.30% 0.00% 0.00% NA
Tropical Japonica  504 26.20% 73.80% 0.00% 0.00% NA
Japonica Intermediate  241 6.60% 92.90% 0.41% 0.00% NA
VI/Aromatic  96 12.50% 87.50% 0.00% 0.00% NA
Intermediate  90 52.20% 46.70% 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
vg0502469018 A -> G LOC_Os05g05060.1 upstream_gene_variant ; 3978.0bp to feature; MODIFIER silent_mutation Average:72.937; most accessible tissue: Callus, score: 88.731 N N N N
vg0502469018 A -> G LOC_Os05g05070.1 upstream_gene_variant ; 939.0bp to feature; MODIFIER silent_mutation Average:72.937; most accessible tissue: Callus, score: 88.731 N N N N
vg0502469018 A -> G LOC_Os05g05090.1 upstream_gene_variant ; 4085.0bp to feature; MODIFIER silent_mutation Average:72.937; most accessible tissue: Callus, score: 88.731 N N N N
vg0502469018 A -> G LOC_Os05g05080.1 downstream_gene_variant ; 1746.0bp to feature; MODIFIER silent_mutation Average:72.937; most accessible tissue: Callus, score: 88.731 N N N N
vg0502469018 A -> G LOC_Os05g05070-LOC_Os05g05080 intergenic_region ; MODIFIER silent_mutation Average:72.937; most accessible tissue: Callus, score: 88.731 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0502469018 NA 3.24E-07 mr1659 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
vg0502469018 NA 1.60E-09 mr1793_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