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Detailed information for vg0318751093:

Variant ID: vg0318751093 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 18751093
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 123. )

Flanking Sequence (100 bp) in Reference Genome:


TGTGGTGGGAAATGGCTTCGAACTTGTTCAAGGTTGCACGGCCGAAGATGGCGTTGTAGTTGTACGGGATGTCGACAACGTCGAACAATACTTGCTCTTC[G/A]
CGTCTGTTTTCCGCCGTGCGGAAGGCTACCATCAACTGTGCTTGGCCAAGAACTTGAACTGCTTCTCCGCTGAAACGTCGGAGCGATGCTGGTGCTGGGG

Reverse complement sequence

CCCCAGCACCAGCATCGCTCCGACGTTTCAGCGGAGAAGCAGTTCAAGTTCTTGGCCAAGCACAGTTGATGGTAGCCTTCCGCACGGCGGAAAACAGACG[C/T]
GAAGAGCAAGTATTGTTCGACGTTGTCGACATCCCGTACAACTACAACGCCATCTTCGGCCGTGCAACCTTGAACAAGTTCGAAGCCATTTCCCACCACA

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 93.90% 0.80% 5.04% 0.34% NA
All Indica  2759 89.60% 1.30% 8.52% 0.58% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 65.70% 4.20% 28.24% 1.85% NA
Indica II  465 96.60% 0.40% 2.80% 0.22% NA
Indica III  913 99.90% 0.00% 0.11% 0.00% NA
Indica Intermediate  786 91.60% 1.10% 6.74% 0.51% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 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 96.70% 0.00% 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
vg0318751093 G -> A LOC_Os03g32749.1 synonymous_variant ; p.Arg682Arg; LOW synonymous_codon Average:52.47; most accessible tissue: Zhenshan97 flag leaf, score: 80.373 N N N N
vg0318751093 G -> DEL LOC_Os03g32749.1 N frameshift_variant Average:52.47; most accessible tissue: Zhenshan97 flag leaf, score: 80.373 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0318751093 NA 9.36E-08 Spikelet_length Ind_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0318751093 4.59E-06 NA mr1864 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