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Detailed information for vg0827379782:

Variant ID: vg0827379782 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 27379782
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, others allele: 0.00, population size: 126. )

Flanking Sequence (100 bp) in Reference Genome:


ACTGATATATATACTGAGATTAATAAAGTCATTATAGGTATCTCATAGTCGACGGGTATGTCACTTACCACTAAAAGAATAATTAGTCGTAAATATAACT[A/G]
TATAAGCATCAGTATCAAGTCTAACACTTGAACCCAGATAGGTCACCTAAAAAATATAATCAGTTAAGCTACGCTCACTTCGCCGCTCAATTAATAATTT

Reverse complement sequence

AAATTATTAATTGAGCGGCGAAGTGAGCGTAGCTTAACTGATTATATTTTTTAGGTGACCTATCTGGGTTCAAGTGTTAGACTTGATACTGATGCTTATA[T/C]
AGTTATATTTACGACTAATTATTCTTTTAGTGGTAAGTGACATACCCGTCGACTATGAGATACCTATAATGACTTTATTAATCTCAGTATATATATCAGT

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 91.40% 8.60% 0.02% 0.00% NA
All Indica  2759 85.70% 14.30% 0.04% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 99.30% 0.70% 0.00% 0.00% NA
Indica I  595 91.90% 8.10% 0.00% 0.00% NA
Indica II  465 95.50% 4.50% 0.00% 0.00% NA
Indica III  913 75.20% 24.60% 0.11% 0.00% NA
Indica Intermediate  786 87.30% 12.70% 0.00% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 90.00% 10.00% 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
vg0827379782 A -> G LOC_Os08g43320.1 upstream_gene_variant ; 747.0bp to feature; MODIFIER silent_mutation Average:68.365; most accessible tissue: Callus, score: 85.438 N N N N
vg0827379782 A -> G LOC_Os08g43334.1 downstream_gene_variant ; 983.0bp to feature; MODIFIER silent_mutation Average:68.365; most accessible tissue: Callus, score: 85.438 N N N N
vg0827379782 A -> G LOC_Os08g43334.2 downstream_gene_variant ; 3083.0bp to feature; MODIFIER silent_mutation Average:68.365; most accessible tissue: Callus, score: 85.438 N N N N
vg0827379782 A -> G LOC_Os08g43320-LOC_Os08g43334 intergenic_region ; MODIFIER silent_mutation Average:68.365; most accessible tissue: Callus, score: 85.438 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0827379782 6.41E-06 1.28E-07 mr1004_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
vg0827379782 NA 7.67E-06 mr1004_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