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Detailed information for vg0407212383:

Variant ID: vg0407212383 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 7212383
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.03, others allele: 0.00, population size: 227. )

Flanking Sequence (100 bp) in Reference Genome:


TGGTGGAATATTATTATTCTAACAAATATATGCATTGCAAGCATCACTAATTCTCCTCTATTTTGGTAATATTGACGGTCGAAATTGATCAATAACGACC[G/A]
TCAACAAAACCCCCCAAGCTTGAACCTTTGCTCGTCCCGAGTGAAGAACGAAAGGAAACAGAGACAGTGTTTGTTGATCAGGAGCTGCTACTATGCTATA

Reverse complement sequence

TATAGCATAGTAGCAGCTCCTGATCAACAAACACTGTCTCTGTTTCCTTTCGTTCTTCACTCGGGACGAGCAAAGGTTCAAGCTTGGGGGGTTTTGTTGA[C/T]
GGTCGTTATTGATCAATTTCGACCGTCAATATTACCAAAATAGAGGAGAATTAGTGATGCTTGCAATGCATATATTTGTTAGAATAATAATATTCCACCA

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 54.50% 44.80% 0.68% 0.00% NA
All Indica  2759 85.70% 13.20% 1.09% 0.00% NA
All Japonica  1512 1.30% 98.60% 0.07% 0.00% NA
Aus  269 43.10% 56.90% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 75.10% 24.50% 0.43% 0.00% NA
Indica III  913 77.90% 19.90% 2.19% 0.00% NA
Indica Intermediate  786 90.30% 8.70% 1.02% 0.00% NA
Temperate Japonica  767 0.30% 99.60% 0.13% 0.00% NA
Tropical Japonica  504 2.80% 97.20% 0.00% 0.00% NA
Japonica Intermediate  241 1.70% 98.30% 0.00% 0.00% NA
VI/Aromatic  96 36.50% 63.50% 0.00% 0.00% NA
Intermediate  90 44.40% 54.40% 1.11% 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
vg0407212383 G -> A LOC_Os04g13070.1 upstream_gene_variant ; 3016.0bp to feature; MODIFIER silent_mutation Average:34.004; most accessible tissue: Zhenshan97 flag leaf, score: 48.165 N N N N
vg0407212383 G -> A LOC_Os04g13080.1 downstream_gene_variant ; 1518.0bp to feature; MODIFIER silent_mutation Average:34.004; most accessible tissue: Zhenshan97 flag leaf, score: 48.165 N N N N
vg0407212383 G -> A LOC_Os04g13070-LOC_Os04g13080 intergenic_region ; MODIFIER silent_mutation Average:34.004; most accessible tissue: Zhenshan97 flag leaf, score: 48.165 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0407212383 NA 1.31E-07 mr1321_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
vg0407212383 NA 1.64E-16 mr1836_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
vg0407212383 3.59E-06 NA mr1865_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
vg0407212383 NA 3.37E-09 mr1946_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
vg0407212383 NA 3.37E-09 mr1948_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