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Detailed information for vg1013821799:

Variant ID: vg1013821799 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 13821799
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, A: 0.00, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:


CAAGCCATTTCAATGGTCTAAAACGTCAAATAGTTATATCAAATTCCGAAGGGAGTATATATATGACGGATATAACACCCCGGTCATTTATATATAAGAA[G/A]
TACACACACTAAAATTAAAACAAAAATCATAATTGTTACCAAGAATTAGTTGCGCTATGAATATCCTTGATAGTACCAAAGTGGTACCATGATCCATATA

Reverse complement sequence

TATATGGATCATGGTACCACTTTGGTACTATCAAGGATATTCATAGCGCAACTAATTCTTGGTAACAATTATGATTTTTGTTTTAATTTTAGTGTGTGTA[C/T]
TTCTTATATATAAATGACCGGGGTGTTATATCCGTCATATATATACTCCCTTCGGAATTTGATATAACTATTTGACGTTTTAGACCATTGAAATGGCTTG

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 81.80% 17.30% 0.87% 0.00% NA
All Indica  2759 69.40% 29.20% 1.38% 0.00% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 37.60% 59.80% 2.52% 0.00% NA
Indica II  465 68.60% 29.90% 1.51% 0.00% NA
Indica III  913 91.00% 8.80% 0.22% 0.00% NA
Indica Intermediate  786 69.00% 29.30% 1.78% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 87.80% 8.90% 3.33% 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
vg1013821799 G -> A LOC_Os10g26520.1 upstream_gene_variant ; 1677.0bp to feature; MODIFIER silent_mutation Average:61.305; most accessible tissue: Callus, score: 78.26 N N N N
vg1013821799 G -> A LOC_Os10g26510-LOC_Os10g26520 intergenic_region ; MODIFIER silent_mutation Average:61.305; most accessible tissue: Callus, score: 78.26 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1013821799 2.73E-06 NA mr1533_2 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
vg1013821799 2.37E-06 5.58E-07 mr1533_2 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