\

Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0507887823:

Variant ID: vg0507887823 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 7887823
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, A: 0.04, others allele: 0.00, population size: 218. )

Flanking Sequence (100 bp) in Reference Genome:


TCGTCCGACGACGGCAAACACCTCCTCGTCGACATACACGAAGGGGTCTGTGGGTCAGATGCCGCCGGTCGTACATTGGTCGGAAAAGCCTTTCGACAAG[A/G]
ATTTTTCTGGCCAACCGCCCTCAAAGACACTTGCGACATGGTACAACGGTGTGAAGCTTGCCAATTTCATAGCAAACACACAAAACTACCAGCGCAAGCA

Reverse complement sequence

TGCTTGCGCTGGTAGTTTTGTGTGTTTGCTATGAAATTGGCAAGCTTCACACCGTTGTACCATGTCGCAAGTGTCTTTGAGGGCGGTTGGCCAGAAAAAT[T/C]
CTTGTCGAAAGGCTTTTCCGACCAATGTACGACCGGCGGCATCTGACCCACAGACCCCTTCGTGTATGTCGACGAGGAGGTGTTTGCCGTCGTCGGACGA

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 56.20% 43.60% 0.28% 0.00% NA
All Indica  2759 84.20% 15.40% 0.40% 0.00% NA
All Japonica  1512 1.70% 98.30% 0.00% 0.00% NA
Aus  269 98.10% 1.90% 0.00% 0.00% NA
Indica I  595 96.60% 2.50% 0.84% 0.00% NA
Indica II  465 68.60% 31.20% 0.22% 0.00% NA
Indica III  913 83.20% 16.40% 0.33% 0.00% NA
Indica Intermediate  786 85.00% 14.80% 0.25% 0.00% NA
Temperate Japonica  767 1.80% 98.20% 0.00% 0.00% NA
Tropical Japonica  504 2.00% 98.00% 0.00% 0.00% NA
Japonica Intermediate  241 0.80% 99.20% 0.00% 0.00% NA
VI/Aromatic  96 1.00% 99.00% 0.00% 0.00% NA
Intermediate  90 45.60% 52.20% 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
vg0507887823 A -> G LOC_Os05g14110.1 missense_variant ; p.Glu1397Gly; MODERATE nonsynonymous_codon ; E1397G Average:56.071; most accessible tissue: Minghui63 flag leaf, score: 77.494 benign -0.569 TOLERATED 1.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0507887823 3.96E-10 4.63E-35 mr1039 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
vg0507887823 5.86E-09 5.06E-10 mr1039 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
vg0507887823 NA 1.15E-11 mr1514 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
vg0507887823 8.44E-09 1.48E-38 mr1632 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
vg0507887823 1.54E-07 9.92E-11 mr1632 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
vg0507887823 NA 6.05E-06 mr1832 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
vg0507887823 NA 1.64E-08 mr1986 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
vg0507887823 1.30E-12 1.74E-36 mr1039_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
vg0507887823 4.09E-09 7.94E-09 mr1039_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
vg0507887823 NA 2.88E-13 mr1514_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
vg0507887823 6.87E-12 1.60E-45 mr1632_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
vg0507887823 1.49E-08 2.98E-10 mr1632_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