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Detailed information for vg0212800520:

Variant ID: vg0212800520 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 12800520
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.91, G: 0.08, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:


AGAGAGTTTTTTGAGTTGGGGATGAATGGGGATGAGATGGGAGAGGGTAGGTGCGGGATGGAGAAGAAAAGGGGCAAAACTGCCTGGGCCCACCTCGACC[G/A]
GTCAGACCGGCCCTATTCGGCCGGTCAGACCGCCGCACCTGGCCGGTCAGACCGCCAGGCCCCCTGCCGGCTGTGCACAGCCCTTGCACAAGCCGGCAAC

Reverse complement sequence

GTTGCCGGCTTGTGCAAGGGCTGTGCACAGCCGGCAGGGGGCCTGGCGGTCTGACCGGCCAGGTGCGGCGGTCTGACCGGCCGAATAGGGCCGGTCTGAC[C/T]
GGTCGAGGTGGGCCCAGGCAGTTTTGCCCCTTTTCTTCTCCATCCCGCACCTACCCTCTCCCATCTCATCCCCATTCATCCCCAACTCAAAAAACTCTCT

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 64.00% 35.60% 0.40% 0.00% NA
All Indica  2759 97.40% 2.10% 0.51% 0.00% NA
All Japonica  1512 1.90% 98.00% 0.13% 0.00% NA
Aus  269 91.40% 7.40% 1.12% 0.00% NA
Indica I  595 98.50% 0.50% 1.01% 0.00% NA
Indica II  465 97.20% 2.60% 0.22% 0.00% NA
Indica III  913 97.20% 2.80% 0.00% 0.00% NA
Indica Intermediate  786 97.10% 2.00% 0.89% 0.00% NA
Temperate Japonica  767 1.30% 98.60% 0.13% 0.00% NA
Tropical Japonica  504 2.40% 97.60% 0.00% 0.00% NA
Japonica Intermediate  241 2.50% 97.10% 0.41% 0.00% NA
VI/Aromatic  96 24.00% 76.00% 0.00% 0.00% NA
Intermediate  90 43.30% 56.70% 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
vg0212800520 G -> A LOC_Os02g21560.1 intron_variant ; MODIFIER silent_mutation Average:41.742; most accessible tissue: Minghui63 young leaf, score: 70.655 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0212800520 NA 1.15E-08 mr1005 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
vg0212800520 NA 2.72E-09 mr1336 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
vg0212800520 NA 3.23E-08 mr1604 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
vg0212800520 7.44E-06 NA mr1620 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
vg0212800520 NA 1.50E-11 mr1636 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
vg0212800520 NA 1.05E-20 mr1838 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
vg0212800520 NA 9.06E-18 mr1336_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