Search for Variation information by Variation ID:

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

Detailed information for vg1116240057:

Variant ID: vg1116240057 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 16240057
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:


CGAACAGAGAGGGGAGGTGGTTCGGCAATTTGAACTTGTGCTTGAGCTTGAGCAGCGGCGACGGAGGCTTTATCGTACTCAGCTTGTATAGCTTGTCGTC[G/T]
CTTAGAATCCTTCTCACCCCTTGCGAACCCGTCAATGATGCGAAGTAGATGCTCGAGCGTCTGCGGCTCCTTGTTGGTGATTTTTCTTGTTAGTTCGCCC

Reverse complement sequence

GGGCGAACTAACAAGAAAAATCACCAACAAGGAGCCGCAGACGCTCGAGCATCTACTTCGCATCATTGACGGGTTCGCAAGGGGTGAGAAGGATTCTAAG[C/A]
GACGACAAGCTATACAAGCTGAGTACGATAAAGCCTCCGTCGCCGCTGCTCAAGCTCAAGCACAAGTTCAAATTGCCGAACCACCTCCCCTCTCTGTTCG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 73.90% 24.80% 0.80% 0.47% NA
All Indica  2759 58.20% 41.70% 0.07% 0.00% NA
All Japonica  1512 99.30% 0.70% 0.00% 0.00% NA
Aus  269 78.10% 0.40% 13.38% 8.18% NA
Indica I  595 42.90% 57.10% 0.00% 0.00% NA
Indica II  465 62.80% 37.20% 0.00% 0.00% NA
Indica III  913 59.60% 40.40% 0.00% 0.00% NA
Indica Intermediate  786 65.50% 34.20% 0.25% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 98.20% 1.80% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 86.70% 13.30% 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
vg1116240057 G -> T LOC_Os11g28250.1 synonymous_variant ; p.Arg509Arg; LOW synonymous_codon Average:24.082; most accessible tissue: Zhenshan97 flag leaf, score: 55.285 N N N N
vg1116240057 G -> DEL LOC_Os11g28250.1 N frameshift_variant Average:24.082; most accessible tissue: Zhenshan97 flag leaf, score: 55.285 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1116240057 1.70E-06 1.70E-06 mr1601 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
vg1116240057 NA 8.50E-06 mr1837 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
vg1116240057 NA 1.98E-06 mr1152_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
vg1116240057 NA 6.30E-07 mr1154_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