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Detailed information for vg0406620827:

Variant ID: vg0406620827 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 6620827
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.84, A: 0.16, others allele: 0.00, population size: 86. )

Flanking Sequence (100 bp) in Reference Genome:


ATTCAACTGAGCTCCGGTTAGAGTTTTGCTAGCATAGCAGACTGCGTGTTGCTTTTTATCCTTAGTTTGGCCCAAGACCACACCAACAGCGAAATCGCTT[G/A]
CATCACACATGATCTCGAAGGGTAGAGTCCAATCAGGGGGTTGGATGATTGGAGCAGAGACGAGTGCCTTTTTGAGAATCTCAAAGGATTTTAGGCACAC

Reverse complement sequence

GTGTGCCTAAAATCCTTTGAGATTCTCAAAAAGGCACTCGTCTCTGCTCCAATCATCCAACCCCCTGATTGGACTCTACCCTTCGAGATCATGTGTGATG[C/T]
AAGCGATTTCGCTGTTGGTGTGGTCTTGGGCCAAACTAAGGATAAAAAGCAACACGCAGTCTGCTATGCTAGCAAAACTCTAACCGGAGCTCAGTTGAAT

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 43.20% 39.50% 0.78% 16.50% NA
All Indica  2759 15.70% 58.80% 1.30% 24.14% NA
All Japonica  1512 99.10% 0.50% 0.00% 0.40% NA
Aus  269 1.10% 72.10% 0.00% 26.77% NA
Indica I  595 1.50% 81.50% 1.34% 15.63% NA
Indica II  465 23.70% 66.90% 0.65% 8.82% NA
Indica III  913 26.20% 34.80% 1.31% 37.68% NA
Indica Intermediate  786 9.70% 64.80% 1.65% 23.92% NA
Temperate Japonica  767 99.30% 0.50% 0.00% 0.13% NA
Tropical Japonica  504 99.00% 0.60% 0.00% 0.40% NA
Japonica Intermediate  241 98.30% 0.40% 0.00% 1.24% NA
VI/Aromatic  96 55.20% 15.60% 1.04% 28.12% NA
Intermediate  90 57.80% 32.20% 0.00% 10.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0406620827 G -> DEL N N silent_mutation Average:30.599; most accessible tissue: Minghui63 flag leaf, score: 61.847 N N N N
vg0406620827 G -> A LOC_Os04g12050.1 downstream_gene_variant ; 1398.0bp to feature; MODIFIER silent_mutation Average:30.599; most accessible tissue: Minghui63 flag leaf, score: 61.847 N N N N
vg0406620827 G -> A LOC_Os04g12040-LOC_Os04g12050 intergenic_region ; MODIFIER silent_mutation Average:30.599; most accessible tissue: Minghui63 flag leaf, score: 61.847 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0406620827 NA 2.29E-07 mr1071 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
vg0406620827 NA 4.42E-13 mr1239 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
vg0406620827 NA 1.93E-06 mr1613 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
vg0406620827 NA 2.75E-10 mr1071_2 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
vg0406620827 6.15E-06 4.51E-12 mr1613_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
vg0406620827 NA 1.26E-06 mr1619_2 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