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Detailed information for vg0821379569:

Variant ID: vg0821379569 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 21379569
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:


ATGTTGTATACTAACATGGATAACCCGCGCGTATATGGATAGTTTCCGTGTACGTCAAGGAAATCTATCCCGTGATAGAAGCAGAATCTACGGATGGGTG[G/A]
AGTCCTACTCGGACGAGGTTGGGTTTTTACCATATCGTGAGGGGTCCGATATCTCCGAGTTCTACTTGGAGATCAACTGACCCGCGGTATATAAGGGACC

Reverse complement sequence

GGTCCCTTATATACCGCGGGTCAGTTGATCTCCAAGTAGAACTCGGAGATATCGGACCCCTCACGATATGGTAAAAACCCAACCTCGTCCGAGTAGGACT[C/T]
CACCCATCCGTAGATTCTGCTTCTATCACGGGATAGATTTCCTTGACGTACACGGAAACTATCCATATACGCGCGGGTTATCCATGTTAGTATACAACAT

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 93.60% 3.20% 3.26% 0.00% NA
All Indica  2759 89.10% 5.40% 5.55% 0.00% NA
All Japonica  1512 99.90% 0.00% 0.07% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 72.90% 11.90% 15.13% 0.00% NA
Indica II  465 98.50% 0.00% 1.51% 0.00% NA
Indica III  913 96.30% 3.30% 0.44% 0.00% NA
Indica Intermediate  786 87.30% 6.10% 6.62% 0.00% NA
Temperate Japonica  767 99.90% 0.00% 0.13% 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  96 100.00% 0.00% 0.00% 0.00% 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
vg0821379569 G -> A LOC_Os08g34100.1 downstream_gene_variant ; 1630.0bp to feature; MODIFIER silent_mutation Average:72.433; most accessible tissue: Minghui63 panicle, score: 82.797 N N N N
vg0821379569 G -> A LOC_Os08g34090-LOC_Os08g34100 intergenic_region ; MODIFIER silent_mutation Average:72.433; most accessible tissue: Minghui63 panicle, score: 82.797 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0821379569 NA 1.16E-06 mr1138 Ind_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
vg0821379569 NA 2.52E-06 mr1354 Ind_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
vg0821379569 NA 1.05E-10 mr1707 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
vg0821379569 NA 4.34E-07 mr1707 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
vg0821379569 6.44E-06 1.29E-12 mr1728 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
vg0821379569 NA 2.08E-08 mr1728 Ind_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
vg0821379569 NA 1.94E-08 mr1860 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