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Detailed information for vg0523223119:

Variant ID: vg0523223119 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 23223119
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGATCCCACCCTAAATTTGTTCACCATGTCACATTGAACGTTTGAACATCTGCATGAAGTATTAAATATAGGCTAAAAATAACTAATTGCACAGATTGCG[A/G]
CTAATTTGCGAGACGAATCTTTTAAGCCTAATTGCTCCATGATTTGACAATGTGGTGCTACAGTAAACAATCGCTGGTTTACGGACGGATTATGTAATTA

Reverse complement sequence

TAATTACATAATCCGTCCGTAAACCAGCGATTGTTTACTGTAGCACCACATTGTCAAATCATGGAGCAATTAGGCTTAAAAGATTCGTCTCGCAAATTAG[T/C]
CGCAATCTGTGCAATTAGTTATTTTTAGCCTATATTTAATACTTCATGCAGATGTTCAAACGTTCAATGTGACATGGTGAACAAATTTAGGGTGGGATCT

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 96.50% 3.50% 0.00% 0.00% NA
All Indica  2759 99.80% 0.20% 0.00% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 52.80% 47.20% 0.00% 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 99.80% 0.20% 0.00% 0.00% NA
Indica Intermediate  786 99.50% 0.50% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 66.70% 33.30% 0.00% 0.00% NA
Intermediate  90 97.80% 2.20% 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
vg0523223119 A -> G LOC_Os05g39570.1 upstream_gene_variant ; 2055.0bp to feature; MODIFIER silent_mutation Average:40.059; most accessible tissue: Zhenshan97 flower, score: 67.623 N N N N
vg0523223119 A -> G LOC_Os05g39560.1 downstream_gene_variant ; 3836.0bp to feature; MODIFIER silent_mutation Average:40.059; most accessible tissue: Zhenshan97 flower, score: 67.623 N N N N
vg0523223119 A -> G LOC_Os05g39560-LOC_Os05g39570 intergenic_region ; MODIFIER silent_mutation Average:40.059; most accessible tissue: Zhenshan97 flower, score: 67.623 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0523223119 4.38E-06 NA mr1559 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
vg0523223119 NA 3.43E-06 mr1808 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
vg0523223119 NA 4.56E-08 mr1989 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
vg0523223119 NA 7.61E-07 mr1126_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
vg0523223119 NA 8.14E-09 mr1166_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
vg0523223119 NA 4.61E-06 mr1603_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
vg0523223119 NA 9.86E-13 mr1612_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
vg0523223119 NA 1.40E-06 mr1815_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