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Detailed information for vg0824350881:

Variant ID: vg0824350881 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 24350881
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATATAATTAAGAAAAACTATTTACCGATCTATTTATCTTAGAGTTTCGCTCCAATCTAAAGTTTCATTTCTCGCGTATAAATTCAAAATTCTTCTTTGTC[G/A]
AAGATTCATCCTAGCTTAGCAACACTCACGGTGGATAAAGCAGCCCATGCTCTGGTTTCTATTTTTTGTGGTTTTTTTTATCAAAGTATTCTTTGTTTTT

Reverse complement sequence

AAAAACAAAGAATACTTTGATAAAAAAAACCACAAAAAATAGAAACCAGAGCATGGGCTGCTTTATCCACCGTGAGTGTTGCTAAGCTAGGATGAATCTT[C/T]
GACAAAGAAGAATTTTGAATTTATACGCGAGAAATGAAACTTTAGATTGGAGCGAAACTCTAAGATAAATAGATCGGTAAATAGTTTTTCTTAATTATAT

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 94.20% 5.60% 0.17% 0.00% NA
All Indica  2759 99.80% 0.20% 0.00% 0.00% NA
All Japonica  1512 82.60% 16.90% 0.53% 0.00% NA
Aus  269 100.00% 0.00% 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 99.70% 0.30% 0.00% 0.00% NA
Indica Intermediate  786 99.60% 0.40% 0.00% 0.00% NA
Temperate Japonica  767 97.50% 2.30% 0.13% 0.00% NA
Tropical Japonica  504 59.30% 39.70% 0.99% 0.00% NA
Japonica Intermediate  241 83.80% 15.40% 0.83% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 95.60% 4.40% 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
vg0824350881 G -> A LOC_Os08g38480.1 upstream_gene_variant ; 846.0bp to feature; MODIFIER silent_mutation Average:28.795; most accessible tissue: Minghui63 panicle, score: 50.413 N N N N
vg0824350881 G -> A LOC_Os08g38470.1 downstream_gene_variant ; 2853.0bp to feature; MODIFIER silent_mutation Average:28.795; most accessible tissue: Minghui63 panicle, score: 50.413 N N N N
vg0824350881 G -> A LOC_Os08g38470-LOC_Os08g38480 intergenic_region ; MODIFIER silent_mutation Average:28.795; most accessible tissue: Minghui63 panicle, score: 50.413 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0824350881 NA 1.04E-07 mr1518 Jap_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
vg0824350881 NA 6.89E-08 mr1676 Jap_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
vg0824350881 1.58E-06 3.80E-18 mr1769 Jap_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
vg0824350881 NA 1.06E-08 mr1676_2 Jap_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
vg0824350881 NA 2.26E-18 mr1769_2 Jap_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