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Detailed information for vg0811614155:

Variant ID: vg0811614155 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 11614155
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: 263. )

Flanking Sequence (100 bp) in Reference Genome:


ACGAAGCAGAAGAACTACACGCACAACAGGAAGCCGAACGACGCCAACTGGAAGAGGAACGCCAAGCACAAGAGCGAGAATGGCTGCAGCGTGAGCAACA[G/A]
GAACGCGAACGGGCTGCAAAGGAGGCTGAGGACCGGTGACAACGGGCCTTGGATGCCGGGCGACGAGCACGAGAACTTATCGGGCAGCAAGACGTCAAGG

Reverse complement sequence

CCTTGACGTCTTGCTGCCCGATAAGTTCTCGTGCTCGTCGCCCGGCATCCAAGGCCCGTTGTCACCGGTCCTCAGCCTCCTTTGCAGCCCGTTCGCGTTC[C/T]
TGTTGCTCACGCTGCAGCCATTCTCGCTCTTGTGCTTGGCGTTCCTCTTCCAGTTGGCGTCGTTCGGCTTCCTGTTGTGCGTGTAGTTCTTCTGCTTCGT

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 96.30% 3.70% 0.00% 0.00% NA
All Indica  2759 99.70% 0.30% 0.00% 0.00% NA
All Japonica  1512 89.90% 10.10% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 99.60% 0.40% 0.00% 0.00% NA
Indica Intermediate  786 99.50% 0.50% 0.00% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 73.20% 26.80% 0.00% 0.00% NA
Japonica Intermediate  241 93.40% 6.60% 0.00% 0.00% NA
VI/Aromatic  96 92.70% 7.30% 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
vg0811614155 G -> A LOC_Os08g19440.1 synonymous_variant ; p.Gln215Gln; LOW synonymous_codon Average:56.092; most accessible tissue: Zhenshan97 flag leaf, score: 80.799 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0811614155 NA 1.93E-06 mr1218 Jap_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
vg0811614155 2.32E-06 1.52E-10 mr1583 Jap_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
vg0811614155 NA 9.42E-07 mr1835 Jap_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