Search for Variation information by Variation ID:

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

Detailed information for vg0820314365:

Variant ID: vg0820314365 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 20314365
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ACTTCTCAAGGCAGCTGTGCTCATGGTAAGTGAAAAAGTCGTTCATGTTTAATACTCTCTTCGTCTCTAAATATTTGACGCCGTTGATTTTTTAAAACAT[G/A]
TTTGATTGTTCGTCCTATTCAAAAACTTTTGTAAAATATGTAAAATTATATGTATACATAAAAGTATATTTAACAATGAATCAAATGATAGGAAAATAAT

Reverse complement sequence

ATTATTTTCCTATCATTTGATTCATTGTTAAATATACTTTTATGTATACATATAATTTTACATATTTTACAAAAGTTTTTGAATAGGACGAACAATCAAA[C/T]
ATGTTTTAAAAAATCAACGGCGTCAAATATTTAGAGACGAAGAGAGTATTAAACATGAACGACTTTTTCACTTACCATGAGCACAGCTGCCTTGAGAAGT

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 93.70% 6.10% 0.21% 0.00% NA
All Indica  2759 92.10% 7.60% 0.29% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 72.90% 26.40% 0.74% 0.00% NA
Indica I  595 96.30% 2.70% 1.01% 0.00% NA
Indica II  465 97.80% 2.20% 0.00% 0.00% NA
Indica III  913 89.00% 11.00% 0.00% 0.00% NA
Indica Intermediate  786 89.20% 10.60% 0.25% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 95.60% 4.40% 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
vg0820314365 G -> A LOC_Os08g32780.1 intron_variant ; MODIFIER silent_mutation Average:43.055; most accessible tissue: Zhenshan97 flower, score: 74.708 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0820314365 NA 8.32E-08 mr1171 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
vg0820314365 NA 1.71E-06 mr1171 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
vg0820314365 NA 6.81E-06 mr1500 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
vg0820314365 5.40E-06 NA mr1524 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
vg0820314365 NA 3.18E-06 mr1544 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
vg0820314365 NA 4.79E-06 mr1952 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
vg0820314365 NA 2.05E-06 mr1996_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