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Detailed information for vg0518191135:

Variant ID: vg0518191135 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 18191135
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: 331. )

Flanking Sequence (100 bp) in Reference Genome:


TGGAATCAGTAACTGAGAATTCTCAAGATCCTTATTTTGCTTGAGGATGAGAGGCAACGAAGTCAACTGCCGTTTTGATGGAGTCAATCTTCTCTGCCTC[G/A]
TTATCTGGGATCTCGAAGCCAAATTCTTCCTCAAAGGCCATGACAATCTCAACTGTATCCAAGCTATCAAGTCCGAGGTCCTTCTGGAAATGAGCATTTG

Reverse complement sequence

CAAATGCTCATTTCCAGAAGGACCTCGGACTTGATAGCTTGGATACAGTTGAGATTGTCATGGCCTTTGAGGAAGAATTTGGCTTCGAGATCCCAGATAA[C/T]
GAGGCAGAGAAGATTGACTCCATCAAAACGGCAGTTGACTTCGTTGCCTCTCATCCTCAAGCAAAATAAGGATCTTGAGAATTCTCAGTTACTGATTCCA

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 97.30% 1.60% 1.06% 0.00% NA
All Indica  2759 95.50% 2.70% 1.78% 0.00% NA
All Japonica  1512 99.90% 0.00% 0.07% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 82.50% 10.60% 6.89% 0.00% NA
Indica II  465 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 97.70% 1.30% 1.02% 0.00% NA
Temperate Japonica  767 99.90% 0.00% 0.13% 0.00% 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
vg0518191135 G -> A LOC_Os05g31290.1 synonymous_variant ; p.Asn107Asn; LOW synonymous_codon Average:63.376; most accessible tissue: Minghui63 panicle, score: 73.225 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0518191135 NA 1.58E-07 mr1709 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
vg0518191135 1.92E-07 NA mr1980 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
vg0518191135 7.85E-06 7.85E-06 mr1821_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