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Detailed information for vg0516073587:

Variant ID: vg0516073587 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 16073587
Reference Allele: CAlternative Allele: T,A
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 377. )

Flanking Sequence (100 bp) in Reference Genome:


CACAGTTCATAAGGATAGCCGGCACCGGTTTTTCAACAATAGGCAGATCCATTAATAGATCACGCAGCCATTCTGCCTCAACAGTAGCAGTATCCAGTGC[C/T,A]
GTCAGTTCTGCTTCCATGGTTGACCTCGTCAAAATAGTCTGATTGCAAGACCTCCAGGAAACAGCACCACCACCCAGTGTGAAGACATATCCACTAGTGG

Reverse complement sequence

CCACTAGTGGATATGTCTTCACACTGGGTGGTGGTGCTGTTTCCTGGAGGTCTTGCAATCAGACTATTTTGACGAGGTCAACCATGGAAGCAGAACTGAC[G/A,T]
GCACTGGATACTGCTACTGTTGAGGCAGAATGGCTGCGTGATCTATTAATGGATCTGCCTATTGTTGAAAAACCGGTGCCGGCTATCCTTATGAACTGTG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 97.00% 3.00% 0.04% 0.00% NA
All Indica  2759 94.90% 5.10% 0.07% 0.00% 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 98.50% 1.50% 0.00% 0.00% NA
Indica II  465 98.70% 1.30% 0.00% 0.00% NA
Indica III  913 91.20% 8.80% 0.00% 0.00% NA
Indica Intermediate  786 94.00% 5.70% 0.25% 0.00% 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  90 100.00% 0.00% 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
vg0516073587 C -> T LOC_Os05g27630.1 synonymous_variant ; p.Thr939Thr; LOW synonymous_codon Average:30.517; most accessible tissue: Zhenshan97 root, score: 47.644 N N N N
vg0516073587 C -> A LOC_Os05g27630.1 synonymous_variant ; p.Thr939Thr; LOW N Average:30.517; most accessible tissue: Zhenshan97 root, score: 47.644 N N N N
vg0516073587 C -> A LOC_Os05g27620.1 downstream_gene_variant ; 3602.0bp to feature; MODIFIER N Average:30.517; most accessible tissue: Zhenshan97 root, score: 47.644 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0516073587 NA 9.34E-06 mr1119 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
vg0516073587 5.35E-06 NA mr1119_2 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
vg0516073587 NA 1.31E-06 mr1144_2 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