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Detailed information for vg0506849318:

Variant ID: vg0506849318 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 6849318
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: 277. )

Flanking Sequence (100 bp) in Reference Genome:


CCTTGTGTGATAGGAATATGAAACAGCTGGCCGATATAAGTAAATGCAATTACACATGGTTTTATAAAAGTAATGTGAAAACATGATTTTATACAGGTCC[G/A]
AGGACCATGGGCAGATCTTGCACAGCAGGGCTCTTCTCCGGTCATGCAACAAGACTCTTTAACCAATAATATAGAGAACAGATGGGTGCAGTAGATTTAG

Reverse complement sequence

CTAAATCTACTGCACCCATCTGTTCTCTATATTATTGGTTAAAGAGTCTTGTTGCATGACCGGAGAAGAGCCCTGCTGTGCAAGATCTGCCCATGGTCCT[C/T]
GGACCTGTATAAAATCATGTTTTCACATTACTTTTATAAAACCATGTGTAATTGCATTTACTTATATCGGCCAGCTGTTTCATATTCCTATCACACAAGG

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 89.20% 10.70% 0.06% 0.00% NA
All Indica  2759 82.10% 17.80% 0.11% 0.00% NA
All Japonica  1512 99.50% 0.50% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 94.80% 5.20% 0.00% 0.00% NA
Indica II  465 71.00% 29.00% 0.00% 0.00% NA
Indica III  913 74.40% 25.60% 0.00% 0.00% NA
Indica Intermediate  786 87.90% 11.70% 0.38% 0.00% NA
Temperate Japonica  767 99.60% 0.40% 0.00% 0.00% NA
Tropical Japonica  504 99.00% 1.00% 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 93.30% 6.70% 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
vg0506849318 G -> A LOC_Os05g11980.1 intron_variant ; MODIFIER silent_mutation Average:34.521; most accessible tissue: Callus, score: 70.096 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0506849318 1.04E-72 2.50E-125 mr1039 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
vg0506849318 3.81E-56 6.66E-93 mr1039 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
vg0506849318 2.08E-25 1.25E-42 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
vg0506849318 2.78E-21 8.98E-30 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
vg0506849318 2.46E-90 3.27E-137 mr1039_2 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
vg0506849318 2.54E-65 2.31E-99 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
vg0506849318 7.27E-11 2.41E-18 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
vg0506849318 1.53E-09 3.42E-10 mr1514_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
vg0506849318 1.27E-44 2.48E-68 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
vg0506849318 1.82E-34 2.37E-49 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
vg0506849318 1.29E-09 NA mr1873_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
vg0506849318 2.96E-08 3.29E-10 mr1873_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