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Detailed information for vg0527589314:

Variant ID: vg0527589314 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 27589314
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, A: 0.03, others allele: 0.00, population size: 89. )

Flanking Sequence (100 bp) in Reference Genome:


CAGCGATGCAGCGGCCATGCCCTTCCTCTCAGGTGCAGGCGCCGGCGTTGCTCCAAGCGGCGATGCAGCCGCCGTCCTCTTCCTCGCAGGCGTCGGCGTC[G/A]
GCGTTGTTCCAGGGGGCGCCCGCACGTCGACCACCGCCTCCTCGATTTGGGGCCGACGGCCCTCTGCGCCCCGCACCGCCGCCTCGCCGTCGTCTCGGTC

Reverse complement sequence

GACCGAGACGACGGCGAGGCGGCGGTGCGGGGCGCAGAGGGCCGTCGGCCCCAAATCGAGGAGGCGGTGGTCGACGTGCGGGCGCCCCCTGGAACAACGC[C/T]
GACGCCGACGCCTGCGAGGAAGAGGACGGCGGCTGCATCGCCGCTTGGAGCAACGCCGGCGCCTGCACCTGAGAGGAAGGGCATGGCCGCTGCATCGCTG

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 51.80% 47.40% 0.74% 0.00% NA
All Indica  2759 69.60% 29.80% 0.62% 0.00% NA
All Japonica  1512 29.20% 70.80% 0.00% 0.00% NA
Aus  269 3.00% 91.10% 5.95% 0.00% NA
Indica I  595 85.20% 13.60% 1.18% 0.00% NA
Indica II  465 50.80% 49.00% 0.22% 0.00% NA
Indica III  913 74.00% 25.70% 0.22% 0.00% NA
Indica Intermediate  786 63.90% 35.20% 0.89% 0.00% NA
Temperate Japonica  767 1.70% 98.30% 0.00% 0.00% NA
Tropical Japonica  504 78.20% 21.80% 0.00% 0.00% NA
Japonica Intermediate  241 14.10% 85.90% 0.00% 0.00% NA
VI/Aromatic  96 35.40% 64.60% 0.00% 0.00% NA
Intermediate  90 51.10% 46.70% 2.22% 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
vg0527589314 G -> A LOC_Os05g48130.1 synonymous_variant ; p.Ser53Ser; LOW synonymous_codon Average:27.253; most accessible tissue: Minghui63 panicle, score: 59.629 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0527589314 NA 2.64E-06 mr1502 Jap_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
vg0527589314 NA 1.11E-06 mr1518 Jap_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
vg0527589314 NA 5.60E-07 mr1543 Jap_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
vg0527589314 NA 3.56E-07 mr1676 Jap_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
vg0527589314 NA 2.21E-06 mr1742 Jap_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
vg0527589314 NA 5.99E-06 mr1817 Jap_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
vg0527589314 NA 3.11E-07 mr1422_2 Jap_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