Search for Variation information by Variation ID:

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

Detailed information for vg0816790944:

Variant ID: vg0816790944 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 16790944
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GCCCAACCAGCCCAGGTTTTGGCTGGCGGCCTCCTCCGTTGTTTCTCTTTGCAGACTTGTGAATTTTGGCCCAATTCATCGTGTCATTTCTGAGTTCTTG[G/A]
CCCATTCATACATAAGTCTGATTCTCAACATCGTCCGATTGATTTATCGTCTGATTTGATGTCGATTCTCCTCCACTTAATGATTATTCTCTGCAAAAGG

Reverse complement sequence

CCTTTTGCAGAGAATAATCATTAAGTGGAGGAGAATCGACATCAAATCAGACGATAAATCAATCGGACGATGTTGAGAATCAGACTTATGTATGAATGGG[C/T]
CAAGAACTCAGAAATGACACGATGAATTGGGCCAAAATTCACAAGTCTGCAAAGAGAAACAACGGAGGAGGCCGCCAGCCAAAACCTGGGCTGGTTGGGC

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 98.90% 0.50% 0.04% 0.53% NA
All Indica  2759 98.20% 0.90% 0.07% 0.87% NA
All Japonica  1512 99.90% 0.00% 0.00% 0.07% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 93.30% 2.80% 0.00% 3.87% NA
Indica III  913 99.80% 0.10% 0.00% 0.11% NA
Indica Intermediate  786 98.00% 1.10% 0.25% 0.64% NA
Temperate Japonica  767 99.90% 0.00% 0.00% 0.13% NA
Tropical Japonica  504 100.00% 0.00% 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 98.90% 1.10% 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
vg0816790944 G -> A LOC_Os08g27520.1 downstream_gene_variant ; 208.0bp to feature; MODIFIER silent_mutation Average:34.57; most accessible tissue: Zhenshan97 flag leaf, score: 64.768 N N N N
vg0816790944 G -> A LOC_Os08g27530.1 downstream_gene_variant ; 2304.0bp to feature; MODIFIER silent_mutation Average:34.57; most accessible tissue: Zhenshan97 flag leaf, score: 64.768 N N N N
vg0816790944 G -> A LOC_Os08g27500-LOC_Os08g27520 intergenic_region ; MODIFIER silent_mutation Average:34.57; most accessible tissue: Zhenshan97 flag leaf, score: 64.768 N N N N
vg0816790944 G -> DEL N N silent_mutation Average:34.57; most accessible tissue: Zhenshan97 flag leaf, score: 64.768 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0816790944 3.04E-06 3.04E-06 mr1501_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