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Detailed information for vg0406361102:

Variant ID: vg0406361102 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 6361102
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 227. )

Flanking Sequence (100 bp) in Reference Genome:


CTGGCTGCTGATGGTTGCTCGCTTTCTCGGCATCGAACTCCTTGCGGAGGGCTTGCACTTCTACAACCGCCATCACAGCTTTGCCCGCACGGTCTGTTCT[G/A]
AACTTTCTCCAAGTTATGGGGGCTTGGCCTTGCCTCGGCGGCTGTCCTTGGATCGCCGGCTGAGACTGGCGAACGAAGAGGGGAGGTGGTTCGGCAACTT

Reverse complement sequence

AAGTTGCCGAACCACCTCCCCTCTTCGTTCGCCAGTCTCAGCCGGCGATCCAAGGACAGCCGCCGAGGCAAGGCCAAGCCCCCATAACTTGGAGAAAGTT[C/T]
AGAACAGACCGTGCGGGCAAAGCTGTGATGGCGGTTGTAGAAGTGCAAGCCCTCCGCAAGGAGTTCGATGCCGAGAAAGCGAGCAACCATCAGCAGCCAG

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 91.00% 9.00% 0.04% 0.00% NA
All Indica  2759 85.00% 14.90% 0.07% 0.00% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 83.50% 16.30% 0.17% 0.00% NA
Indica II  465 88.00% 11.80% 0.22% 0.00% NA
Indica III  913 88.60% 11.40% 0.00% 0.00% NA
Indica Intermediate  786 80.20% 19.80% 0.00% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 99.40% 0.60% 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 91.10% 8.90% 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
vg0406361102 G -> A LOC_Os04g11620.1 synonymous_variant ; p.Phe650Phe; LOW synonymous_codon Average:42.546; most accessible tissue: Zhenshan97 flag leaf, score: 67.31 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0406361102 NA 3.63E-08 mr1846 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
vg0406361102 4.03E-06 NA mr1062_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
vg0406361102 2.27E-07 6.56E-08 mr1062_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
vg0406361102 9.61E-06 1.98E-06 mr1169_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
vg0406361102 NA 7.26E-07 mr1169_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
vg0406361102 NA 1.25E-06 mr1608_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
vg0406361102 NA 6.97E-07 mr1882_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
vg0406361102 NA 3.67E-06 mr1882_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