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Detailed information for vg0715862869:

Variant ID: vg0715862869 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 15862869
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 109. )

Flanking Sequence (100 bp) in Reference Genome:


TAAACACAGAGAGAAGCAATAAAGTTGTCATCTACTTTGAGAGTTCTTCTATTTGTGTTTCACCGGGTTTCGGCGGTCTAACCGGCATCTCACCGGCGGT[C/T]
AGACTGGCGACCTACTGGCGGTCAAACCGACTAAGGCGAGGCGGTCAGACCGGTGGCGGCGACAGCGACTTCAGACGCGGCAGACGATCTTCAGGCGGTT

Reverse complement sequence

AACCGCCTGAAGATCGTCTGCCGCGTCTGAAGTCGCTGTCGCCGCCACCGGTCTGACCGCCTCGCCTTAGTCGGTTTGACCGCCAGTAGGTCGCCAGTCT[G/A]
ACCGCCGGTGAGATGCCGGTTAGACCGCCGAAACCCGGTGAAACACAAATAGAAGAACTCTCAAAGTAGATGACAACTTTATTGCTTCTCTCTGTGTTTA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 95.60% 4.40% 0.00% 0.00% NA
All Indica  2759 92.70% 7.30% 0.00% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 84.50% 15.50% 0.00% 0.00% NA
Indica II  465 99.10% 0.90% 0.00% 0.00% NA
Indica III  913 95.10% 4.90% 0.00% 0.00% NA
Indica Intermediate  786 92.20% 7.80% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 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 95.60% 4.40% 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
vg0715862869 C -> T LOC_Os07g27290.1 synonymous_variant ; p.Val184Val; LOW synonymous_codon Average:45.21; most accessible tissue: Zhenshan97 root, score: 57.64 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0715862869 1.06E-07 1.56E-11 mr1059 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
vg0715862869 8.27E-06 1.68E-09 mr1167 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
vg0715862869 1.47E-06 3.23E-10 mr1535 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
vg0715862869 1.66E-07 1.11E-11 mr1675 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
vg0715862869 NA 2.08E-08 mr1950 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