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Detailed information for vg0523265069:

Variant ID: vg0523265069 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 23265069
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.79, A: 0.20, others allele: 0.00, population size: 76. )

Flanking Sequence (100 bp) in Reference Genome:


CCTCGCTGACGAAGTAGACAGGCCGCTGCACCTTTCGGGGGGGCCGGTTCGTGCTGTCAAGGGCTGGTAACTCGGGGCGCACCTGTTCGGAGGTCCTGGG[G/A]
GGATCCCAGACTGCCTCGGGATCATCAAGCTCAGGGCCACCTGCCAAAGCCTCCGCTCCTCCCTTGGGGGCCTCGGGGCCCTCCTGGGGGCTAGAAGCTT

Reverse complement sequence

AAGCTTCTAGCCCCCAGGAGGGCCCCGAGGCCCCCAAGGGAGGAGCGGAGGCTTTGGCAGGTGGCCCTGAGCTTGATGATCCCGAGGCAGTCTGGGATCC[C/T]
CCCAGGACCTCCGAACAGGTGCGCCCCGAGTTACCAGCCCTTGACAGCACGAACCGGCCCCCCCGAAAGGTGCAGCGGCCTGTCTACTTCGTCAGCGAGG

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 60.70% 39.10% 0.21% 0.00% NA
All Indica  2759 90.80% 9.00% 0.29% 0.00% NA
All Japonica  1512 1.50% 98.50% 0.07% 0.00% NA
Aus  269 96.30% 3.70% 0.00% 0.00% NA
Indica I  595 92.90% 6.70% 0.34% 0.00% NA
Indica II  465 93.80% 6.00% 0.22% 0.00% NA
Indica III  913 87.80% 12.20% 0.00% 0.00% NA
Indica Intermediate  786 90.70% 8.70% 0.64% 0.00% NA
Temperate Japonica  767 0.70% 99.30% 0.00% 0.00% NA
Tropical Japonica  504 2.00% 98.00% 0.00% 0.00% NA
Japonica Intermediate  241 2.90% 96.70% 0.41% 0.00% NA
VI/Aromatic  96 40.60% 59.40% 0.00% 0.00% NA
Intermediate  90 51.10% 47.80% 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
vg0523265069 G -> A LOC_Os05g39620.1 synonymous_variant ; p.Pro709Pro; LOW synonymous_codon Average:58.566; most accessible tissue: Zhenshan97 panicle, score: 74.671 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0523265069 NA 3.09E-10 Grain_weight 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
vg0523265069 NA 2.04E-31 mr1243 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
vg0523265069 NA 2.18E-16 mr1484 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
vg0523265069 NA 2.27E-35 mr1542 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
vg0523265069 NA 2.60E-22 mr1548 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
vg0523265069 NA 1.64E-17 mr1566 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
vg0523265069 8.19E-06 6.42E-42 mr1591 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
vg0523265069 NA 1.35E-13 mr1592 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
vg0523265069 NA 6.40E-06 mr1750 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
vg0523265069 1.31E-06 1.44E-39 mr1828 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
vg0523265069 NA 8.26E-10 mr1905 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
vg0523265069 NA 1.20E-17 mr1342_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
vg0523265069 NA 2.68E-07 mr1683_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