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Detailed information for vg0220406103:

Variant ID: vg0220406103 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 20406103
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 126. )

Flanking Sequence (100 bp) in Reference Genome:


TAATTGACTTTAGATGGTGCTAAATGCAGTTTTAGTAGCATGTTGTTCTGGCCTTCTACGCATTCCGGGTATCTCCGTTTATTTTTTTTTTTGCATAGAC[C/A]
ATTCAAAAGGTGAATCATCTGTATATATGAACATTAATCGTCTTTGAATATATTTTTGTTATATATATACACACACATGAAGGATTAAATTTGGAGTCCA

Reverse complement sequence

TGGACTCCAAATTTAATCCTTCATGTGTGTGTATATATATAACAAAAATATATTCAAAGACGATTAATGTTCATATATACAGATGATTCACCTTTTGAAT[G/T]
GTCTATGCAAAAAAAAAAATAAACGGAGATACCCGGAATGCGTAGAAGGCCAGAACAACATGCTACTAAAACTGCATTTAGCACCATCTAAAGTCAATTA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 90.60% 9.30% 0.08% 0.00% NA
All Indica  2759 91.70% 8.20% 0.07% 0.00% NA
All Japonica  1512 99.40% 0.60% 0.00% 0.00% NA
Aus  269 26.40% 72.90% 0.74% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 73.10% 26.70% 0.22% 0.00% NA
Indica III  913 96.50% 3.50% 0.00% 0.00% NA
Indica Intermediate  786 91.00% 8.90% 0.13% 0.00% NA
Temperate Japonica  767 99.60% 0.40% 0.00% 0.00% NA
Tropical Japonica  504 99.00% 1.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 95.80% 4.20% 0.00% 0.00% NA
Intermediate  90 96.70% 3.30% 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
vg0220406103 C -> A LOC_Os02g34120.1 downstream_gene_variant ; 2277.0bp to feature; MODIFIER silent_mutation Average:25.294; most accessible tissue: Minghui63 flag leaf, score: 30.782 N N N N
vg0220406103 C -> A LOC_Os02g34100-LOC_Os02g34120 intergenic_region ; MODIFIER silent_mutation Average:25.294; most accessible tissue: Minghui63 flag leaf, score: 30.782 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0220406103 NA 6.58E-07 mr1114 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
vg0220406103 NA 5.69E-06 mr1174 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
vg0220406103 3.01E-06 3.01E-06 mr1396 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