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Detailed information for vg0403565641:

Variant ID: vg0403565641 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 3565641
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.61, G: 0.39, others allele: 0.00, population size: 92. )

Flanking Sequence (100 bp) in Reference Genome:


GCTTCATTCCATGCCACTCCGTCTCCCCGAAGCCGCGCGTCGTCAGTTCATCCCCCTCGCTCCGTTTGCTCGCACGCATCTGGCAGTCGTCGGCGATCTC[A/G]
TCCTCCCCAACGCCCGCGAGCTCGTCCTTCCCCACGTCGGCAAGCTCCTTCCCCATGCCGGCAAGCTTTTTTTTGCGAATGACGGCGAGCTCTTCCTTCC

Reverse complement sequence

GGAAGGAAGAGCTCGCCGTCATTCGCAAAAAAAAGCTTGCCGGCATGGGGAAGGAGCTTGCCGACGTGGGGAAGGACGAGCTCGCGGGCGTTGGGGAGGA[T/C]
GAGATCGCCGACGACTGCCAGATGCGTGCGAGCAAACGGAGCGAGGGGGATGAACTGACGACGCGCGGCTTCGGGGAGACGGAGTGGCATGGAATGAAGC

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 58.50% 41.30% 0.21% 0.00% NA
All Indica  2759 78.80% 20.90% 0.29% 0.00% NA
All Japonica  1512 13.80% 86.20% 0.00% 0.00% NA
Aus  269 88.50% 10.80% 0.74% 0.00% NA
Indica I  595 96.80% 2.70% 0.50% 0.00% NA
Indica II  465 73.10% 26.50% 0.43% 0.00% NA
Indica III  913 73.40% 26.40% 0.22% 0.00% NA
Indica Intermediate  786 74.80% 25.10% 0.13% 0.00% NA
Temperate Japonica  767 3.10% 96.90% 0.00% 0.00% NA
Tropical Japonica  504 13.90% 86.10% 0.00% 0.00% NA
Japonica Intermediate  241 47.30% 52.70% 0.00% 0.00% NA
VI/Aromatic  96 92.70% 7.30% 0.00% 0.00% NA
Intermediate  90 63.30% 36.70% 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
vg0403565641 A -> G LOC_Os04g06780.1 synonymous_variant ; p.Asp35Asp; LOW synonymous_codon Average:53.509; most accessible tissue: Zhenshan97 young leaf, score: 77.422 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0403565641 2.12E-06 2.12E-06 mr1061 Jap_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
vg0403565641 NA 1.43E-06 mr1528_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